There cannot be a conflict between ingame and user made foliage cos the ingame id system is different from user made. Ingame files are .ai and user made foliage would be a .ucs. You cannot delete the outer wall and gate without having the map editor in the game.
Maybe Caddie when he comes in can show you what he does since I am not that familiar. Or if you are a member of DD you could ask Jay directly. He is good at rewording things so you understand.