BuildCraft version: 7.99.15-pre4
Forge version: 1.12.2-14.23.1.2590
Link to crash report or log: N/A
Singleplayer or multiplayer: Both

Items that are not used in the auto workbench recipe are able to enter via automation. I tested with hoppers and pipes where neither were able to put items that are not in the recipe into the auto-workbench. This is one of the setups I used:

Basically #3334 in 7.99.15-pre4

This is one of those things I think the player could have solved themselves instead of having BuildCraft solve it for them.