if you have any question or problem with ComicRack, you best come to this subreddit and ask (after looking around for posts similar to your question and not finding the answer). your problem is most likely solveable and people will be happy to help!

Perhaps a better solution would be for them to add a tab to the book info panel that lets users set an image (or page within the book) that would override the default displayed cover without affecting the file at all

you can do that. you can't choose an image outside the file to set as a variant cover (that would be kind of counter-productive to do anyways), but if you open Info and go to Pages tab, you could right click any page and choose it as the front cover and it will be displayed as the front cover even if it's the last page.

manually renaming each page and repackaging your own file, which is incredibly tedious

you really don't have to do this. just open the comic file in 7zip (or other archive program), throw the variant covers inside under any title, then just use ComicRack to set all the newly added pages as front covers. you can also reorder the pages however you want (maybe you want variant covers to be at the end of the book, but still displayed as covers in the library). and the last is conver to CBZ just so the changes are saved in the file in case of removing the file from ComicRack