I like the sound of the Kindle approach, too. It means that you could vary the use of your "document percentage," exporting a relatively large part of the text each time. You could use bookmarks, for example, then jump and export one file per quote. Something like that?
And now something else has really made me rather cross.

Does exporting the highlights also mean
deleting them from the reader? Because, after having done my little experiment, they have simply vanished!