I still don't understand what the Mountain of Skulls represented

The early trappers and pelt dealers absolutely decimated buffalo herds collecting their skins. Those skull piles were a sadly common scene. Glass was probably haunted by images of what various scouting/ trapping parties he'd been a member of had been up to.

Guilt maybe? Leo hung around the Native Americans a lot and had a son with one of them. Native Americans were much more conservative when it came to hunting, and lots of settler populations were not. His job was hunting and butchering animals 24/7, so if he had any empathy for the animals, or the environment, or the native american philosophies, it would certainly result in him feeling some amount of guilt.

Just my guess...

That's a part of the movie I never understood, myself. I'm sure there is some meaning behind it, but I can't come to a logical conclusion. Or, maybe I'm looking too hard for the logic. KingCobra has a good reply though.