### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
if (in_top_left_triangle) {
						ret += Vector2i(-1, 0);
					} else if (in_bottom_left_triangle) {
						ret += Vector2i(-1, 1);
					}
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_RIGHT:
					ret = Vector2(ret.x / 2 - ret.y, ret.y + ret.x / 2).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(0, -1);
					} else if (in_bottom_left_triangle) {
						ret += Vector2i(-1, 0);
					}
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_DOWN:
					ret = Vector2(ret.x / 2 + ret.y, ret.y - ret.x / 2).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(-1, 0);
					} else if (in_bottom_left_triangle) {
						ret += Vector2i(0, 1);
					}
					break;
			}
		}
	} else {
		ret = (ret + Vector2(0.00005, 0.00005)).floor();
	}
	return Vector2i(ret);
}
bool TileMap::is_existing_neighbor(TileSet::CellNeighbor p_cell_neighbor) const {