### 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)
HashMap<Vector2i, TileSet::TerrainsPattern> output;
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND_V(!tile_set.is_valid(), output);
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), output);
	
	Vector<TileSet::CellNeighbor> neighbor_list;
	for (int i = 0; i < p_coords_array.size() - 1; i++) {
		
		TileSet::CellNeighbor found_bit = TileSet::CELL_NEIGHBOR_MAX;
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_map_node->is_existing_neighbor(bit)) {
				if (tile_map_node->get_neighbor_cell(p_coords_array[i], bit) == p_coords_array[i + 1]) {
					found_bit = bit;
					break;
				}
			}
		}
		ERR_FAIL_COND_V_MSG(found_bit == TileSet::CELL_NEIGHBOR_MAX, output, vformat("Invalid terrain path, %s is not a neighboring tile of %s", p_coords_array[i + 1], p_coords_array[i]));
		neighbor_list.push_back(found_bit);
	}
	
	Vector<Vector2i> can_modify_list;
	RBSet<Vector2i> can_modify_set;