while the clipping is defiantly a frustrating thing, its something that's prevalent in nearly all games.
Ark, survival evolved show cases how much of a joke it can truly be. Developers do the best they can, but there is no realistic system that sees the surface and player or NPC objects interacting with a solid object accurately.
For now, us players have to adjust to the sometimes maddening clipping issue in some games. maybe in the future a game engine will come out that can accurately simulate this. but for now.

would suggest making allowance's for the issue and build your place with the advice given above.

me, I flatten an area then build a trench outside it. I also try and build on a mountain/hill type. flatten the top. leaving steep walls. then dig my trenches around that.
have found that approach very effective, but time consuming.

this is my current build. i cant make trenches yet, but you can see the plan i have. this might give you some ideas for your own game.

https://steamcommunity.com/sharedfiles/filedetails/?id=2906817204