Custom configuration for a SVG QR based on points and the position pattern with colors.

create-qr.php

<?php

$result = Builder::create()
            ->writer(new CustomSvgWriter())
            ->writerOptions(['compact' => false, 'style' => 'dot'])
            ->data('text To QR')
            ->encoding(new Encoding('UTF-8'))
            ->errorCorrectionLevel(ErrorCorrectionLevel::High)
            ->size(300)
            ->margin(10)
            ->roundBlockSizeMode(RoundBlockSizeMode::Margin)
            ->validateResult(false)
            ->build();

return $result->getString();

CustomSvgWriter.php

<?php

declare(strict_types=1);

namespace App\Services;

use Endroid\QrCode\Bacon\MatrixFactory;
use Endroid\QrCode\ImageData\LogoImageData;
use Endroid\QrCode\Label\LabelInterface;
use Endroid\QrCode\Logo\LogoInterface;
use Endroid\QrCode\Matrix\MatrixInterface;
use Endroid\QrCode\QrCodeInterface;
use Endroid\QrCode\Writer\Result\ResultInterface;
use Endroid\QrCode\Writer\Result\SvgResult;
use Endroid\QrCode\Writer\WriterInterface;

// Fue necesario customizar esta clase completa para personalizar el QR
final class CustomSvgWriter implements WriterInterface
{
    public const DECIMAL_PRECISION = 2;
    public const WRITER_OPTION_COMPACT = 'compact';
    public const WRITER_OPTION_BLOCK_ID = 'block_id';
    public const WRITER_OPTION_EXCLUDE_XML_DECLARATION = 'exclude_xml_declaration';
    public const WRITER_OPTION_EXCLUDE_SVG_WIDTH_AND_HEIGHT = 'exclude_svg_width_and_height';
    public const WRITER_OPTION_FORCE_XLINK_HREF = 'force_xlink_href';

    // Possible values: 'rect', 'dot'
    public const WRITER_OPTION_DEFINITION_STYLE = 'style';

    public function write(QrCodeInterface $qrCode, LogoInterface $logo = null, LabelInterface $label = null, array $options = []): ResultInterface
    {
        if (!isset($options[self::WRITER_OPTION_COMPACT])) {
            $options[self::WRITER_OPTION_COMPACT] = true;
        }

        if (!isset($options[self::WRITER_OPTION_BLOCK_ID])) {
            $options[self::WRITER_OPTION_BLOCK_ID] = 'block';
        }

        if (!isset($options[self::WRITER_OPTION_EXCLUDE_XML_DECLARATION])) {
            $options[self::WRITER_OPTION_EXCLUDE_XML_DECLARATION] = false;
        }

        if (!isset($options[self::WRITER_OPTION_EXCLUDE_SVG_WIDTH_AND_HEIGHT])) {
            $options[self::WRITER_OPTION_EXCLUDE_SVG_WIDTH_AND_HEIGHT] = false;
        }

        if (!isset($options[self::WRITER_OPTION_DEFINITION_STYLE])) {
            $options[self::WRITER_OPTION_DEFINITION_STYLE] = 'rect';
        }

        $matrixFactory = new MatrixFactory();
        $matrix = $matrixFactory->create($qrCode);

        $xml = new \SimpleXMLElement('<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"/>');
        $xml->addAttribute('version', '1.1');
        if (!$options[self::WRITER_OPTION_EXCLUDE_SVG_WIDTH_AND_HEIGHT]) {
            $xml->addAttribute('width', $matrix->getOuterSize() . 'px');
            $xml->addAttribute('height', $matrix->getOuterSize() . 'px');
        }
        $xml->addAttribute('viewBox', '0 0 ' . $matrix->getOuterSize() . ' ' . $matrix->getOuterSize());

        $background = $xml->addChild('rect');
        $background->addAttribute('x', '0');
        $background->addAttribute('y', '0');
        $background->addAttribute('width', strval($matrix->getOuterSize()));
        $background->addAttribute('height', strval($matrix->getOuterSize()));
        $background->addAttribute('fill', '#' . sprintf('%02x%02x%02x', $qrCode->getBackgroundColor()->getRed(), $qrCode->getBackgroundColor()->getGreen(), $qrCode->getBackgroundColor()->getBlue()));
        $background->addAttribute('fill-opacity', strval($qrCode->getBackgroundColor()->getOpacity()));

        if ($options[self::WRITER_OPTION_COMPACT]) {
            $this->writePath($xml, $qrCode, $matrix);
        } else {
            $this->writeBlockDefinitions($xml, $qrCode, $matrix, $options);
        }

        $result = new SvgResult($matrix, $xml, boolval($options[self::WRITER_OPTION_EXCLUDE_XML_DECLARATION]));

        if ($logo instanceof LogoInterface) {
            $this->addLogo($logo, $result, $options);
        }

        return $result;
    }

    private function writePath(\SimpleXMLElement $xml, QrCodeInterface $qrCode, MatrixInterface $matrix): void
    {
        $path = '';
        for ($rowIndex = 0; $rowIndex < $matrix->getBlockCount(); ++$rowIndex) {
            $left = $matrix->getMarginLeft();
            for ($columnIndex = 0; $columnIndex < $matrix->getBlockCount(); ++$columnIndex) {
                if (1 === $matrix->getBlockValue($rowIndex, $columnIndex)) {
                    // When we are at the first column or when the previous column was 0 set new left
                    if (0 === $columnIndex || 0 === $matrix->getBlockValue($rowIndex, $columnIndex - 1)) {
                        $left = $matrix->getMarginLeft() + $matrix->getBlockSize() * $columnIndex;
                    }
                    // When we are at the
                    if ($columnIndex === $matrix->getBlockCount() - 1 || 0 === $matrix->getBlockValue($rowIndex, $columnIndex + 1)) {
                        $top = $matrix->getMarginLeft() + $matrix->getBlockSize() * $rowIndex;
                        $bottom = $matrix->getMarginLeft() + $matrix->getBlockSize() * ($rowIndex + 1);
                        $right = $matrix->getMarginLeft() + $matrix->getBlockSize() * ($columnIndex + 1);
                        $path .= 'M' . $this->formatNumber($left) . ',' . $this->formatNumber($top);
                        $path .= 'L' . $this->formatNumber($right) . ',' . $this->formatNumber($top);
                        $path .= 'L' . $this->formatNumber($right) . ',' . $this->formatNumber($bottom);
                        $path .= 'L' . $this->formatNumber($left) . ',' . $this->formatNumber($bottom) . 'Z';
                    }
                }
            }
        }

        $pathDefinition = $xml->addChild('path');
        $pathDefinition->addAttribute('fill', '#' . sprintf('%02x%02x%02x', $qrCode->getForegroundColor()->getRed(), $qrCode->getForegroundColor()->getGreen(), $qrCode->getForegroundColor()->getBlue()));
        $pathDefinition->addAttribute('fill-opacity', strval($qrCode->getForegroundColor()->getOpacity()));
        $pathDefinition->addAttribute('d', $path);
    }

    private function getBlockDefinition(\SimpleXMLElement $xml, MatrixInterface $matrix, array $options): ?\SimpleXMLElement
    {
        if (strval($options[self::WRITER_OPTION_DEFINITION_STYLE]) === 'dot') {
            $blockDefinition = $xml->defs->addChild('circle');
            $blockDefinition->addAttribute('id', strval($options[self::WRITER_OPTION_BLOCK_ID]));
            $blockDefinition->addAttribute('cx', $this->formatNumber($matrix->getBlockSize() / 2));
            $blockDefinition->addAttribute('cy', $this->formatNumber($matrix->getBlockSize() / 2));
            $blockDefinition->addAttribute('r', $this->formatNumber($matrix->getBlockSize() / 2));
            return $blockDefinition;
        }

        $blockDefinition = $xml->defs->addChild('rect');
        $blockDefinition->addAttribute('id', strval($options[self::WRITER_OPTION_BLOCK_ID]));
        $blockDefinition->addAttribute('width', $this->formatNumber($matrix->getBlockSize()));
        $blockDefinition->addAttribute('height', $this->formatNumber($matrix->getBlockSize()));
        return $blockDefinition;

    }

    /** @param array<string, mixed> $options */
    private function writeBlockDefinitions(\SimpleXMLElement $xml, QrCodeInterface $qrCode, MatrixInterface $matrix, array $options): void
    {
        $xml->addChild('defs');
        $blockDefinition = $this->getBlockDefinition($xml, $matrix, $options);
        $blockDefinition->addAttribute('fill', '#' . sprintf('%02x%02x%02x', $qrCode->getForegroundColor()->getRed(), $qrCode->getForegroundColor()->getGreen(), $qrCode->getForegroundColor()->getBlue()));
        $blockDefinition->addAttribute('fill-opacity', strval($qrCode->getForegroundColor()->getOpacity()));

        for ($rowIndex = 0; $rowIndex < $matrix->getBlockCount(); ++$rowIndex) {
            for ($columnIndex = 0; $columnIndex < $matrix->getBlockCount(); ++$columnIndex) {
                if ($this->isPatternsPositional($matrix, $rowIndex, $columnIndex)) {
                    continue;
                }
                if (1 === $matrix->getBlockValue($rowIndex, $columnIndex)) {
                    $block = $xml->addChild('use');
                    $block->addAttribute('x', $this->formatNumber($matrix->getMarginLeft() + $matrix->getBlockSize() * $columnIndex));
                    $block->addAttribute('y', $this->formatNumber($matrix->getMarginLeft() + $matrix->getBlockSize() * $rowIndex));
                    $block->addAttribute('xlink:href', '#' . $options[self::WRITER_OPTION_BLOCK_ID], 'http://www.w3.org/1999/xlink');
                }
            }
        }

        # Add the positional patterns
        $this->addPositionalPatterns($xml, $matrix);
    }

    private function isPatternsPositional(MatrixInterface $matrix, $x, $y): bool
    {
        $patternSize = 7; // Positional patterns are typically 7x7 blocks

        // Top-left positional pattern
        if ($x < $patternSize && $y < $patternSize) {
            return true;
        }

        // Top-right positional pattern
        if ($x >= $matrix->getBlockCount() - $patternSize && $y < $patternSize) {
            return true;
        }

        // Bottom-left positional pattern
        if ($x < $patternSize && $y >= $matrix->getBlockCount() - $patternSize) {
            return true;
        }

        return false;
    }

    private function addPositionalPatterns(\SimpleXMLElement $xml, MatrixInterface $matrix)
    {
        $dotDefinition = $xml->defs->addChild('circle');
        $dotDefinition->addAttribute('id', 'positional_patterns_dot');
        $dotDefinition->addAttribute('r', '10');

        $donutDefinition = $xml->defs->addChild('circle');
        $donutDefinition->addAttribute('id', 'positional_patterns_donut');
        $donutDefinition->addAttribute('r', '18');
        $donutDefinition->addAttribute('fill', 'none');
        $donutDefinition->addAttribute('stroke', '#5cbd41');
        $donutDefinition->addAttribute('stroke-width', $this->formatNumber(6));

        # Top-left positional pattern
        $xLeft = $this->formatNumber($matrix->getMarginLeft() + $matrix->getBlockSize() * 3.5);
        $yTop = $xLeft;
        $this->addPositionalPattern($xml, $xLeft, $yTop);

        # Top-right positional pattern
        $xTop = $this->formatNumber($matrix->getMarginLeft() + $matrix->getBlockSize() * ($matrix->getBlockCount() - 3.5));
        $this->addPositionalPattern($xml, $xTop, $xLeft);

        # Bottom-left positional pattern
        $yBottom = $xTop;
        $this->addPositionalPattern($xml, $xLeft, $yBottom);

    }

    private function addPositionalPattern(\SimpleXMLElement $xml, $x, $y)
    {
        $block = $xml->addChild('use');
        $block->addAttribute('x', $x);
        $block->addAttribute('y', $y);
        $block->addAttribute('xlink:href', '#positional_patterns_dot', 'http://www.w3.org/1999/xlink');

        $block = $xml->addChild('use');
        $block->addAttribute('x', $x);
        $block->addAttribute('y', $y);
        $block->addAttribute('xlink:href', '#positional_patterns_donut', 'http://www.w3.org/1999/xlink');
    }

    /** @param array<string, mixed> $options */
    private function addLogo(LogoInterface $logo, SvgResult $result, array $options): void
    {
        $logoImageData = LogoImageData::createForLogo($logo);

        if (!isset($options[self::WRITER_OPTION_FORCE_XLINK_HREF])) {
            $options[self::WRITER_OPTION_FORCE_XLINK_HREF] = false;
        }

        $xml = $result->getXml();

        /** @var \SimpleXMLElement $xmlAttributes */
        $xmlAttributes = $xml->attributes();

        $x = intval($xmlAttributes->width) / 2 - $logoImageData->getWidth() / 2;
        $y = intval($xmlAttributes->height) / 2 - $logoImageData->getHeight() / 2;

        $imageDefinition = $xml->addChild('image');
        $imageDefinition->addAttribute('x', strval($x));
        $imageDefinition->addAttribute('y', strval($y));
        $imageDefinition->addAttribute('width', strval($logoImageData->getWidth()));
        $imageDefinition->addAttribute('height', strval($logoImageData->getHeight()));
        $imageDefinition->addAttribute('preserveAspectRatio', 'none');

        if ($options[self::WRITER_OPTION_FORCE_XLINK_HREF]) {
            $imageDefinition->addAttribute('xlink:href', $logoImageData->createDataUri(), 'http://www.w3.org/1999/xlink');
        } else {
            $imageDefinition->addAttribute('href', $logoImageData->createDataUri());
        }
    }

    private function formatNumber(float $number): string
    {
        $string = number_format($number, self::DECIMAL_PRECISION, '.', '');
        $string = rtrim($string, '0');

        return rtrim($string, '.');
    }
}

Hello after trying it out, I am unsure whether It is my usage that is wrong or it simply doesn't work.
Basically it does generate Dot-based SVG however they are not readable. I've noticed the 3 corners are dots with 3 green circles and I am unsure whether this is the reason for it not being readable, I also couldn't find an option to change that part, perhaps you can clarify it to me? :)

@DeadlykillOfficial The problem is that the patterns are not aligned, it is already fixed.