Ok I was able able to figure out how to get it to farm without worrying about the underground nodes.
In general settings, click on advance settings on the bottom right. I'm not sure if all these work or not, I just enable them and it has been working flawlessly as far as i can from watching it now.
Class/ Fight Class - check the Use lua to move
Looting and Farming option - check detect nodes stuck and blacklist zone where I
Save and Close