The market for a $100 app isn't very large, and that price point is also a target for fraud / scams / accidental purchase complaints. This risk is offset by additional review scrutiny, but the cost for that additional scrutiny is amortized over a small number of potential customers.
The result of all this is that $100 purchases are expensive for Apple to run, and Apple as a rational actor should discourage them. I wouldn't be surprised to learn that the whole $50+ market runs at a loss that is covered by the cheaper apps.