As far as the black mark issue goes, I'd say it's a wise move to do something about the pants. It's only going to get worse with time and I image that most people have him hunched; to fit in a Detolf or just to mimic his on screen stature or whatever.
The black pants definitely serve a purpose so I wouldn't scrap them all together. I re-glued mine at a lower point so they still function but won't ever rub against the belly. I glued it at about 10 points going all the way around as opposed to HT's 4 points.
I agree that it's a good move to do something. However without knowing the manufacturers reason for the black shorts, just glueing them at a lower point may be defeating the purpose/location of the shorts in the first place. Also, the material itself appears to be a cause of some of the stains. So just lowering them may only lower the possible stain area.
This is just my reasoning. I have noticed that the skin underneath the shorts can stain without any friction or movement. If that holds up lowering the shirts may simply spreading the issue to a different area of the legs/thighs.