There's actually a better format than Safari web archives hidden in the Safari Debug menu: Save Page Complete.
This saves the individual files of the site in standard format, html, js, css, etc., much like Chrome does with Webpage, Complete.
Or just use SingleFile (https://www.getsinglefile.com)
With the AI vision tools we have these days, I just export to PDF. At least within the Notes app, the search feature also searches the contents of PDFs.