I would suggest allowing multiple versions for compilation (when specified). There should also be a check that people don't specify multiple versions that can't exist on the same directory (e.g 2.6 and 2.7). Otherwise the compileall module's CLI handles this and people can call it with different interpreters as necessary.

IOW I'm advocating KISS for what the tool does. Since making the zip file is only really tricky bit it should only handle that case. Heck you can make it part of the zipfile module if there is resistance to adding yet another script that python installs (obviously will need a Cheeseshop package for older versions).

Otherwise I like everything else.