The whole thing fit in the title.

I realized there's assembly table support, but EnderIO? No?

EnderIo have own scripts for the machines where you can add or delete some recipes.

As an Example
AlloySmelterRecipes_User.xml
Here you can control all Alloy Smelter recipes.

For the Enchanter using
EnchanterRecipes_User.xml

All files found in configs/enderio/

Due to EnderIO having its own configuration ,support is very low priority currently :)

At the time this was a low priority, but FTB Tweaks doesn't work with configs/non-MT scripts, so I feel one should have the ability to work with FTB Tweaks and EIO.