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Debug bodies shouldn't affect the physics at all, and in my testing they never did. Are you 100% sure this is whats happening?
I tested it again, and yeah.. this is dependant on the debug body for some reason.
I created a completely new object (box.obj), gave it the Q3M Physics behaviour and at the start of the Layout it rotates the physics body 45 degrees. Looks like this with the debug body activated
Ignore the 3D model for now. Well, next the thing I did was to deactivate is the debug body, nothing else, and..
The collision for that object is different now. I can't reach the same spot like in the first image (slightly inside the box). It all works when I activate physics body. Dunno where my error is Maybe I'm understanding something wrong? Sorry for the questioning again!