Machine crafting with ender folders currently will treat the ender folders as a normal folder (takes items out of the ender folder, but the ender folder's cabinet doesn't update to reflect this).

This allows a person to cycle an ender folder between an auto crafter and some method of transferring it to their inventory (Random Things player interface, for example) to create an infinite amount of items as fast as they can craft with the folders, inject them in a player inv, and then take the folder back into the crafter.

Example from Journey Across the Void (1.12 pack, latest version):
Ender folder start

linked cabinet

RFTools Autocrafter inventory setup

Crafter recipe

Some crafting later...

And the folder resets!