Is there a way to set the physics collision mask on a object to use the collision polygons, bounding box, or circle depending on a condition? Or would I need to make a completely separate object/sprite for each mask to do this?
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You can do this with Chipmunk physics, but I don't know if this addon has been ported for C3.
With standard Physics behavior you can probably use an invisible sprite with several frames, each with a different collision polygon. Add physics behavior and change frames when necessary. Pin your main sprite to it.