### 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)
PackedStringArray warnings = Node::get_configuration_warnings();
	
	RBSet<int> y_sorted_z_index;
	for (const Ref<TileMapLayer> &layer : layers) {
		if (layer->is_y_sort_enabled()) {
			y_sorted_z_index.insert(layer->get_z_index());
		}
	}
	
	for (const Ref<TileMapLayer> &layer : layers) {
		if (!layer->is_y_sort_enabled() && y_sorted_z_index.has(layer->get_z_index())) {
			warnings.push_back(RTR("A Y-sorted layer has the same Z-index value as a not Y-sorted layer.\nThis may lead to unwanted behaviors, as a layer that is not Y-sorted will be Y-sorted as a whole with tiles from Y-sorted layers."));
			break;
		}
	}
	if (!is_y_sort_enabled()) {
		
		for (const Ref<TileMapLayer> &layer : layers) {
			if (layer->is_y_sort_enabled()) {
				warnings.push_back(RTR("A TileMap layer is set as Y-sorted, but Y-sort is not enabled on the TileMap node itself."));
				break;
			}
		}
	} else {