To answer your second-to-last question, it would require completely replacing the current code that generates the downloads completely—the current program used is, in computer terms, ancient. It's a very desired feature, but there hasn't been a pair of hands with knowledge and time to gut, replace, and test-to-destruction the new code yet.

As for opt-in, the file is created and stored when the work is first downloaded. To have a "choice" of epubs means creating and storing twice as many files.