you could call upon those files in your migration .py files, inside your upgrade() and downgrade() callables. You can customize how those callables render by editing your script.py.mako file.
However, for the .py file to not be there at all, you'd need to override ScriptDirectory
and Script
right now, unless we made more of a hook to implement extensions like this. Overriding those classes is possible but would likely require monkeypatching at the moment. It's certainly something Alembic could support.