I'm not sure what you're asking. The built in physics engine doesn't care what your graphics look like.
If you're building a game that has a low rez - pixel art style, don't use the scale commands, make sure you still use the size commands to set the sizes of your sprites. This won't effect the physics system at all. If you need to adjust any aspect of the physics system, all physics variables can be adjusted, including physics object's 'weight', the gravity, etc..
If you haven't applied any code yet, than how do you know if anything will go wrong?
I say make a test program, throw together a very simple level, throw in some characters and objects and just add the default physics and see what happens. Than just work from there. If you run into any troubles or feel like the physics don't represent the 'scale' of the objects, come back and post the code and I'm sure the community will be happy to help you out.
