Always struck me as quite odd MHTML fell out of favor. Back in the day when I wanted to preserve a web page it was the logical choice since you could just click "save as archive".
Blame XMLHttpRequest, Flash, JS, and embedded video. It doesn't make sense to archive a document when the necessary interactive content elements will essentially fail when opened offline.
What would be cool is one package with the original HTML file, the fully rendered DOM written out as a second file+assets package, and a PDF just in case the first two get fucked.
You can first prerender the page with Chrome in headless mode (see my other comment), and then convert it into a single document using an inlining tool (such as the OP's). That way the JS will run and render the page (see my other comments here for an example).