### 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)
_rendering_was_cleaned_up = forced_cleanup;
}
void TileMapLayer::_rendering_quadrants_update_cell(CellData &r_cell_data, SelfList<RenderingQuadrant>::List &r_dirty_rendering_quadrant_list) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	
	bool is_valid = false;
	int tile_y_sort_origin = 0;
	TileSetSource *source;
	if (tile_set->has_source(r_cell_data.cell.source_id)) {
		source = *tile_set->get_source(r_cell_data.cell.source_id);
		TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
		if (atlas_source && atlas_source->has_tile(r_cell_data.cell.get_atlas_coords()) && atlas_source->has_alternative_tile(r_cell_data.cell.get_atlas_coords(), r_cell_data.cell.alternative_tile)) {
			is_valid = true;
			const TileData *tile_data;
			if (r_cell_data.runtime_tile_data_cache) {
				tile_data = r_cell_data.runtime_tile_data_cache;
			} else {
				tile_data = atlas_source->get_tile_data(r_cell_data.cell.get_atlas_coords(), r_cell_data.cell.alternative_tile);
			}
			tile_y_sort_origin = tile_data->get_y_sort_origin();
		}
	}
	if (is_valid) {
		
		Vector2 canvas_items_position;
		Vector2i quadrant_coords;
		if (tile_map_node->is_y_sort_enabled() && is_y_sort_enabled()) {
			canvas_items_position = Vector2(0, tile_map_node->map_to_local(r_cell_data.coords).y + tile_y_sort_origin + y_sort_origin);
			quadrant_coords = canvas_items_position * 100;
		} else {