I think trying to come up with a way to save malformed code in an epub (and to consequently open that same malformed code and leave it malformed) through manipulation (auto or otherwise) of the existing Clean Source settings is akin to trying to pick up a turd by the clean end. There just is no easy, all encompassing, automatic method that will make it user friendly and intuitive for everyone.
I've mentioned this before. I think the best solution (if there even has to be a solution) would be to have an alternate file type. You get a warning message when trying to save; "Code not Well-Formed! Click here to fix automatically, click here to return and fix it manually, and click here to save it as a *.garbage file."
Opening a *.garbage file never involves Clean Source or Pretty Print. You get what you get. Opening an existing .*ePub containing errors could give you the option of opening as a *garbage file or auto-correction. You never have to worry about making sure the settings are "just right" before opening a project you may have saved in a "less than optimal" state. When you have the code fixed... save it as an epub. Lather, rinse, repeat as necessary.
Anything that involves a user remembering to make sure certain features are disabled before saving (and consequently opening) an epub are doomed to cause confusion (but is probably the least intrusive). Scenarios that automatically disable settings will cause confusion and anger.
Last edited by DiapDealer; 02-19-2013 at 08:37 AM.