### 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> terrain_fill_output = terrain_fill_path(vector_path, p_terrain_set, p_terrain, p_ignore_empty_terrains);
	for (const KeyValue<Vector2i, TileSet::TerrainsPattern> &kv : terrain_fill_output) {
		if (painted_set.has(kv.key)) {
			
			TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
			set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
		} else {
			
			TileSet::TerrainsPattern in_map_terrain_pattern = TileSet::TerrainsPattern(*tile_set, p_terrain_set);
			TileMapCell cell = get_cell(kv.key);
			if (cell.source_id != TileSet::INVALID_SOURCE) {
				TileSetSource *source = *tile_set->get_source(cell.source_id);
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
				if (atlas_source) {
					
					TileData *tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
					if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
						in_map_terrain_pattern = tile_data->get_terrains_pattern();
					}
				}
			}
			if (in_map_terrain_pattern != kv.value) {
				TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
				set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
			}
		}
	}
}
TypedArray<Vector2i> TileMapLayer::get_used_cells() const {