### 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)
for (KeyValue<Vector2i, CellData> &kv : tile_map) {
			CellData &cell_data = kv.value;
			_debug_quadrants_update_cell(cell_data, dirty_debug_quadrant_list);
		}
	} else {
		
		for (SelfList<CellData> *cell_data_list_element = dirty.cell_list.first(); cell_data_list_element; cell_data_list_element = cell_data_list_element->next()) {
			CellData &cell_data = *cell_data_list_element->self();
			_debug_quadrants_update_cell(cell_data, dirty_debug_quadrant_list);
		}
	}
	
	for (SelfList<DebugQuadrant> *quadrant_list_element = dirty_debug_quadrant_list.first(); quadrant_list_element;) {
		SelfList<DebugQuadrant> *next_quadrant_list_element = quadrant_list_element->next(); 
		DebugQuadrant &debug_quadrant = *quadrant_list_element->self();
		
		bool has_a_tile = false;
		RID &ci = debug_quadrant.canvas_item;
		for (SelfList<CellData> *cell_data_list_element = debug_quadrant.cells.first(); cell_data_list_element; cell_data_list_element = cell_data_list_element->next()) {
			CellData &cell_data = *cell_data_list_element->self();
			if (cell_data.cell.source_id != TileSet::INVALID_SOURCE) {
				has_a_tile = true;
				break;
			}
		}
		if (has_a_tile) {
			
			if (ci.is_valid()) {
				rs->canvas_item_clear(ci);
			} else {