To again voice my opinion...

I would say that if you have imbalances or mobility issues, then trying to correct that by squatting is probably a poor idea. Powerlifters tend to address these issues by doing prehab movements, and I know that Louis Simmons and Dave Tate are big supporters of bringing up weaknesses to support main lifts.

Hence, my original post about barefoot training to strengthen the muscles of the foot. That would be a prime example of one possibility in this great world (certainly not the only possibility) to address fallen arches by some means other than orthotics.