### 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)
Vector2 size_1 = Vector2(1, 1) / tile_set->get_tile_size();
			for (int j = 0; j < polygon.size(); j++) {
				uvs.write[j] = polygon[j] * size_1 + Vector2(0.5, 0.5);
			}
			Vector<Color> color2;
			color2.push_back(Color(1, 1, 1, 0.4));
			p_canvas_item->draw_polygon(polygon, color2, uvs, one_way_icon);
		}
	}
	RenderingServer::get_singleton()->canvas_item_add_set_transform(p_canvas_item->get_canvas_item(), Transform2D());
}
void TileDataTerrainsEditor::_update_terrain_selector() {
	ERR_FAIL_COND(!tile_set.is_valid());
	
	Vector<String> options;
	options.push_back(String(TTR("No terrains")) + String(":-1"));
	for (int i = 0; i < tile_set->get_terrain_sets_count(); i++) {
		options.push_back(vformat("Terrain Set %d", i));
	}
	terrain_set_property_editor->setup(options);
	terrain_set_property_editor->update_property();
	
	int terrain_set = int(dummy_object->get("terrain_set"));
	if (terrain_set == -1) {
		terrain_property_editor->hide();
	} else {
		options.clear();
		Vector<Vector<Ref<Texture2D>>> icons = tile_set->generate_terrains_icons(Size2(16, 16) * EDSCALE);
		options.push_back(String(TTR("No terrain")) + String(":-1"));
		for (int i = 0; i < tile_set->get_terrains_count(terrain_set); i++) {