### 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)
Dictionary dict;
	dict["linear_velocity"] = dummy_object->get("linear_velocity");
	dict["angular_velocity"] = dummy_object->get("angular_velocity");
	Array array;
	for (int i = 0; i < polygon_editor->get_polygon_count(); i++) {
		ERR_FAIL_COND_V(polygon_editor->get_polygon(i).size() < 3, Variant());
		Dictionary polygon_dict;
		polygon_dict["points"] = polygon_editor->get_polygon(i);
		polygon_dict["one_way"] = dummy_object->get(vformat("polygon_%d_one_way", i));
		polygon_dict["one_way_margin"] = dummy_object->get(vformat("polygon_%d_one_way_margin", i));
		array.push_back(polygon_dict);
	}
	dict["polygons"] = array;
	return dict;
}
void TileDataCollisionEditor::_set_painted_value(TileSetAtlasSource *p_tile_set_atlas_source, Vector2 p_coords, int p_alternative_tile) {