My idea is just a .map format. It's just a zip file with two .png's in it (foreground and wallmask), and potentially some .metadata files or something. You get bundling for free, aswell as compression. Python (and I think Java too, but I'm not sure) can read/write zip files with the standard library.
Also, one thing that you must keep in mind, PyGG2 will be using the PNG alpha channel for alpha, and not the green key color. (Yes, this also means you can get semi-transparent sprites).
I also had a (random) idea for the metadata, instead of making it some sort of text file we could make a third image instead. Bright red means RED's spawn, blue means BLUE's spawn, grey means bullet wall, yellow is left-to-right bullet wall, orange is right-to-left bullet wall, you get the idea. This way you also can easily overlay the maps and quickly spot any errors.