If they didn't think of this their idea is broken and the server will either go broke or they'll patch it when they notice. There are several possible patches for this, the first that comes to mind is that they've modded natural emeralds to spawn with a different damage value than emeralds that villagers trade. After that it's pretty easy for their ATM mod to reject if they see villager sourced emeralds. As items with different damage values don't stack they won't mix either.

That's just the first patch that comes to mind for fixing this system. Another would be to just remove villagers/npc trading with a mod.