I don't normally comment on HN, but this topic is something I've got a strong opinion on. I use Foliate to read epub's, but I've got one massive peeve with ALL e-readers. I'd really, really like for an option that tells the e-reader not to modify my epub. I don't use annotations, I really don't need the e-reader to bookmark where I've stopped reading. Just don't write over my epub!
Hmm, I mostly use Calibre for epub reading, and was not aware of it writes bookmark back to epub itself. Do you mean some e-ink reader updates .epub whenever you add bookmark? That seems an odd implementation.
Now I just copy my epub's to a temporary file before reading.