Anyone else have the same problem, when you place a farmhouse. The ground level gets ruined, by either having a hole in the ground, or raised up. Even if I place it on what appears to be a level ground, It will still ruin it.
I believe you can use the FREE PLACE toggle option when building (use F1 to see your controls) and it will not only ignore hitboxes, but it should also ignore terrain and not change it at all. You may still have to paint it to your liking, but if I remember correctly, FREE PLACE will not move the terrain.