>Uh-oh. Why do we have so many distinct versions of The Last Unicorn? Well, each distinct format of a work has its own ISBN (so a hardcover, paperback, and eBook all have different ISBNs),

This isn't even the half of it. On some digital books, I'll find a dozen ISBNs in the front matter. Of course there's the hardback, the clothbound (not always the same as the hardback), the alk. paper variant, paperback, trade paperback, epub, pdf, "Adobe digital", and "master digital e-book" (no idea what that even is myself). And that's all just issued together. If they reprint, it won't get a new ISBN, but if the rights convey to another publisher, that one will get a whole 'nother set again. Some popular titles likely have low hundreds of ISBNs, and keep in mind that these have only been a thing since the late 1960s (9 digit ISBNs, technically just SBNs back then). Then with the now dead paperback trade, you could go through a dozen different covers for the most popular books (King, etc) but they'd all use the same ISBN.

Then, and this one bites me the most... if archive.org scans in a hardback with its ISBN, what do I use for the scanned pdf? I've decided that for lack of a better alternative I have to use it, but if the publisher made their own pdf (even just scanning the hardback), then it is supposed to issue a new ISBN to it.

Cataloging my own library, I've had to use a hodgepodge of unique ids. ASINs, ISBNs, Worldcat's OCLC numbers, Open Library's, and a few others besides. And it still comes up short. The number of oddball publishers and pamphlets and so forth that have never been cataloged anywhere is enormous.