# Default = true
# If set to false, research system will be disabled and
# all recipes will be available in normal crafting station.
B:use_research_system=false

Even though the above is set to false the recipes are still in AW crafting.

It turns out the above config does actually work but adding the gates and NPCs to the config manually doesnt work

That config option does not work for me (AW 2.4.113-beta-MC1.7.10-FULL), I changed that to false, but I'm still not able to craft a tree farm nor in AW crafting table nor in normal one.

Did you reload the game after config change ?

Hmmm... I'm not totally sure what could be happened, but it seems to work for me. After the config change I tried to restart the game, but the treefarm recipe still not worked. But now, after a few reload and a base move, I checked it again, and it seems working. However, too much thing happened (e.g, I broke and re-placed the engineering table, re-crafted the book since I accidentally lost it, and many different things), so I could not tell what solved the problem. Maybe a few more restart.