It's part of the Pawn code, BaseChange() I think. Basically when a Pawn lands on another Pawn, it will jump off to prevent players stacking (Jailbreak turned that off to allow human ladders) and will apply damage to the base Pawn. The damage amount is calculated from the previous falling speed, but is usually relatively small.
There are mods that implement a "Super Mario Mode", i.e. very high stomp damage. Those are probably mutators that check for stomp damage and increase it to the point where it's deadly.