Do the ebooks you're referring to use an image for the ² symbol, rather than css, unicode, or mathjax-generated mathml? A lot of old math books that have been converted from scans do that, for instance, because their OCR was okay at regular text but not good at superscripts, subscripts, or other mathematical symbols.
They use an image in the Kindle version. I don’t know about other versions, but I strongly suspect that the PDF version, if any, doesn’t. These aren’t old books, they are recent nonfiction books from established publishers. They surely don’t use OCR to produce the Kindle version.
I’ve never seen a Kindle book rendering anything as vector graphics. That’s just not a thing in the Kindle world, as far as I can tell. It’s either basic text or pixel images.
One example I just checked is a book from MIT Press from 2021, where even √2 is rendered as an image, and also isn’t scaled correctly with respect to the text size. It really puts you off reading such books in Kindle.
Anyway, I guess my point is that TFA won’t help with what I find the most annoying about the Kindle experience.
A second peeve is that in dark mode you can only have gray on black, not white on black.