Removing core theme builder locations in Elementor. The first file is the original file in Elementor, just for reference. The second is a mu plugin to disable select locations. This must be ran via plugin or mu-plugin, because it runs before themes are loaded.

elementor-mods.php

<?php

/**
 * Plugin Name: Elementor Mods
 * Plugin URI:  https://gist.github.com/bob-moore/986bafade1aa0b04bb30e0a2f08fb105
 * Description: Mod some elementor stuff
 * Version:     0.1.0
 * Author:      Bob Moore
 * Author URI:  https://github.com/bob-moore
 * License:     GPL-2.0+
 * License URI: http://www.gnu.org/licenses/gpl-2.0.txt
 */

/**
 * Remove the action the registers the default document types in the theme builder
 *
 * 1. Get the instance of the types manager, so we can remove the same instance
 * 2. Remove the action
 *
 * @see  elementor-pro/modules/theme-builder/classes/template-types-manager.php
 * @return void
 */
function prefix_unregister_types_manager() {

	if ( ! class_exists( '\\ElementorPro\\Modules\\ThemeBuilder\\Module' ) ) {
		return false;
	}

	$types_manager = \ElementorPro\Modules\ThemeBuilder\Module::instance()->get_types_manager();

	remove_action( 'elementor/documents/register', [$types_manager, 'register_documents']);

}
add_action( 'elementor/init', 'prefix_unregister_types_manager' );

/**
 * Register only the document types you want to allow
 *
 * Copied from the core elementor class. Uncomment each document type you want
 * to be allowed to show
 *
 * @see  elementor-pro/modules/theme-builder/classes/template-types-manager.php
 * @return void
 */
function prefix_register_document_types() {

	if ( ! class_exists( '\\ElementorPro\\Modules\\ThemeBuilder\\Module' ) ) {
		return false;
	}

	$docs_types = [
		'section' => \ElementorPro\Modules\ThemeBuilder\Documents\Section::get_class_full_name(),
		'header' => \ElementorPro\Modules\ThemeBuilder\Documents\Header::get_class_full_name(),
		'footer' => \ElementorPro\Modules\ThemeBuilder\Documents\Footer::get_class_full_name(),
		// 'single' => Documents\Single::get_class_full_name(),
		// 'single-post' => Documents\Single_Post::get_class_full_name(),
		// 'single-page' => Documents\Single_Page::get_class_full_name(),
		// 'archive' => Documents\Archive::get_class_full_name(),
		// 'search-results' => Documents\Search_Results::get_class_full_name(),
		'error-404' => \ElementorPro\Modules\ThemeBuilder\Documents\Error_404::get_class_full_name(),
	];

	foreach ( $docs_types as $type => $class_name ) {
		\Elementor\Plugin::instance()->documents->register_document_type( $type, $class_name );
	}
}
add_action( 'elementor/documents/register', 'prefix_register_document_types' );

templates-types-manager.php

<?php
/**
 * Original file in Elementor
 */
namespace ElementorPro\Modules\ThemeBuilder\Classes;

use ElementorPro\Modules\ThemeBuilder\Documents;
use ElementorPro\Plugin;

if ( ! defined( 'ABSPATH' ) ) {
	exit; // Exit if accessed directly
}

class Templates_Types_Manager {
	private $docs_types = [];

	public function __construct() {
		add_action( 'elementor/documents/register', [ $this, 'register_documents' ] );
	}

	public function get_types_config( $args = [] ) {
		$config = [];

		$document_types = Plugin::elementor()->documents->get_document_types( $args );

		foreach ( $document_types as $type => $document_type ) {
			$properties = $document_type::get_properties();

			if ( ( new $document_type() ) instanceof Documents\Theme_Document ) {
				$config[ $type ] = $properties;
			}
		}

		return $config;
	}

	public function register_documents() {
		$this->docs_types = [
			'section' => Documents\Section::get_class_full_name(),
			'header' => Documents\Header::get_class_full_name(),
			'footer' => Documents\Footer::get_class_full_name(),
			'single' => Documents\Single::get_class_full_name(),
			'single-post' => Documents\Single_Post::get_class_full_name(),
			'single-page' => Documents\Single_Page::get_class_full_name(),
			'archive' => Documents\Archive::get_class_full_name(),
			'search-results' => Documents\Search_Results::get_class_full_name(),
			'error-404' => Documents\Error_404::get_class_full_name(),
		];

		foreach ( $this->docs_types as $type => $class_name ) {
			Plugin::elementor()->documents->register_document_type( $type, $class_name );
		}
	}
}