### 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)
ret = Vector2(ret.x / 2, ret.y * 2 + ret.x);
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_RIGHT:
					ret = Vector2((ret.x + ret.y) / 2, ret.y - ret.x);
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_DOWN:
					ret = Vector2((ret.x - ret.y) / 2, ret.y + ret.x);
					break;
			}
		} else { 
			switch (tile_set->get_tile_layout()) {
				case TileSet::TILE_LAYOUT_STACKED:
					ret = Vector2(ret.x, ret.y + (Math::posmod(ret.x, 2) == 0 ? 0.0 : 0.5));
					break;
				case TileSet::TILE_LAYOUT_STACKED_OFFSET:
					ret = Vector2(ret.x, ret.y + (Math::posmod(ret.x, 2) == 1 ? 0.0 : 0.5));
					break;
				case TileSet::TILE_LAYOUT_STAIRS_RIGHT:
					ret = Vector2(ret.x * 2 + ret.y, ret.y / 2);
					break;
				case TileSet::TILE_LAYOUT_STAIRS_DOWN:
					ret = Vector2(ret.x, ret.y + ret.x / 2);
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_RIGHT:
					ret = Vector2(ret.x + ret.y, (ret.y - ret.x) / 2);
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_DOWN:
					ret = Vector2(ret.x - ret.y, (ret.y + ret.x) / 2);
					break;
			}