Remove Chrome's Custom Search Engines

rmOtherEngines.js

// Go to chrome://settings/searchEngines
// Open the Developer Tools
// Run the following in the Javascript console tab

const otherEngines = document.querySelector("body > settings-ui")
    .shadowRoot.querySelector("#main")
    .shadowRoot.querySelector("settings-basic-page")
    .shadowRoot.querySelector("#basicPage > settings-section.expanded > settings-search-page")
    .shadowRoot.querySelector("#pages > settings-subpage > settings-search-engines-page")
    .shadowRoot.querySelector("#otherEngines").shadowRoot

let n = otherEngines.querySelector('iron-list').childElementCount - 1;
let rmbtn = otherEngines.querySelector('#frb0')
    .shadowRoot.querySelector('#delete')

const sleep = (ms) => new Promise(resolve => setTimeout(resolve, ms));

while (n--) {
    rmbtn.click();
    await sleep(2000); // adjust the sleep duration as you see fit.
}

If you want a permanent solution and don't mind installing an extra chrome extension:

Don't add custom search engines by Greg Sadetsky,