### 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)
dict["terrain_set"] = tile_data->get_terrain_set();
					dict["terrain"] = tile_data->get_terrain();
					Array array;
					for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
						TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
						array.push_back(tile_data->is_valid_terrain_peering_bit(bit) ? tile_data->get_terrain_peering_bit(bit) : -1);
					}
					dict["terrain_peering_bits"] = array;
					drag_modified[cell] = dict;
				}
				tile_data->set_terrain_set(drag_painted_value);
			}
			drag_last_pos = mm->get_position();
			accept_event();
		} else if (drag_type == DRAG_TYPE_PAINT_TERRAIN_BITS) {
			Dictionary painted = Dictionary(drag_painted_value);
			int terrain_set = int(painted["terrain_set"]);
			int terrain = int(painted["terrain"]);
			Vector3i tile = p_tile_atlas_view->get_alternative_tile_at_pos(mm->get_position());
			Vector2i coords = Vector2i(tile.x, tile.y);
			int alternative_tile = tile.z;
			if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
				TileMapCell cell;
				cell.source_id = 0;
				cell.set_atlas_coords(coords);
				cell.alternative_tile = alternative_tile;
				
				TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, alternative_tile);
				if (tile_data->get_terrain_set() == terrain_set) {
					if (!drag_modified.has(cell)) {