Hmm, the palisade seems to be growing neatly along the stone walls so both wall types are supposed to "co-exist"? If so I don't mind getting a palisade's worth of free influence though it still shouldn't have started on it's own unless it's supposed to be included in the stone wall package.
This is the gateway. While there is definitely some clipping the wooden gate provides another "gate layer" along with the stone one, both can be operated independently.
I just wish walls were better explained in the tool-tip.