The sites I have looked at have Zero Pro more expensive than Due, here is 2 examples:
Perhaps Due is priced low (about same price as Mega) because it does not sell much, and they are hoping Zero Pro will be more popular. As it is, it seems to be underpowered or overpriced. Most Cortex M3 chips are cheaper than atmega256, I can't see why the BOM cost justifies the price.