If you're worried about note/highlight exportability and willing to work with an older format with several disadvantages, I think perhaps
eReader's pdb format might work well for you.
The eReader for Mac app I've tried lets you do highlights in 4 colours as well as notes, and will fully export both highlight and note text to plain text.
The notes are kept in separate corresponding files to the individual original .pdb with a certain extension all in the ~/Documents/eReader/Book Data folder (something like that), rather than directly with the book files, and I'm pretty sure you should be able to move them back and forth.
Very likely the eReader for iPhone app will store stuff in much the same way (the eReader for Windows app which I tried via Wine did), and they're really unlikely to change the file format any time soon, since it's practically defunct now and they haven't even updated their software in years.
So as long as they don't yank the downloads, you won't have to worry about suddenly introduced incompatibility.
PDB formatting display can be a little primitive even compared to Mobi, which is pretty backwards, but the format is documented and easy to convert and you'll be mainly reading and fixing older mostly plain-text books if I've read your post right?
It may not be optimal, but maybe worth a try to see if it can work for you.