### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	RenderingServer *rs = RenderingServer::get_singleton();
	
	bool forced_cleanup = in_destructor || !enabled || !tile_map_node->is_inside_tree() || !tile_set.is_valid() || !tile_map_node->is_visible_in_tree();
	
	if (forced_cleanup) {
		
		if (canvas_item.is_valid()) {
			rs->free(canvas_item);
			canvas_item = RID();
		}
	} else {
		
		if (!canvas_item.is_valid()) {
			RID ci = rs->canvas_item_create();
			rs->canvas_item_set_parent(ci, tile_map_node->get_canvas_item());
			canvas_item = ci;
		}
		RID &ci = canvas_item;
		rs->canvas_item_set_draw_index(ci, layer_index_in_tile_map_node - (int64_t)0x80000000);
		rs->canvas_item_set_sort_children_by_y(ci, y_sort_enabled);
		rs->canvas_item_set_use_parent_material(ci, tile_map_node->get_use_parent_material() || tile_map_node->get_material().is_valid());
		rs->canvas_item_set_z_index(ci, z_index);
		rs->canvas_item_set_default_texture_filter(ci, RS::CanvasItemTextureFilter(tile_map_node->get_texture_filter_in_tree()));
		rs->canvas_item_set_default_texture_repeat(ci, RS::CanvasItemTextureRepeat(tile_map_node->get_texture_repeat_in_tree()));
		rs->canvas_item_set_light_mask(ci, tile_map_node->get_light_mask());
		
		Color layer_modulate = modulate;
		int selected_layer = tile_map_node->get_selected_layer();
		if (selected_layer >= 0 && layer_index_in_tile_map_node != selected_layer) {