When you buy a game with source on the scirra store, what are you allowed to do with it?
If I "reskin" it with a different theme, can I publish it and make money from ads?
It depends on the purchase. Usually you're allowed one game per commercial license.
Obviously you would also need a license from Scirra if you plan on editing using the C2 editor.
All purchases have their own license.
What confuses me is scirra has a category for Games with Source and a category for Game Licenses...
Develop games in your browser. Powerful, performant & highly capable.
I believe game license would be for a special case where you are allowed to make more than one product from the files.
Like if you were to make Angry Birds into Angry Zombies with both being commercially viable.
There are some restrictions however.