### 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)
ERR_FAIL_COND(!p_tile_set.is_valid());
	if (tile_set == p_tile_set) {
		return;
	}
	
	clear_polygons();
	if (p_tile_set.is_valid()) {
		Vector<Vector2> polygon = p_tile_set->get_tile_shape_polygon();
		for (int i = 0; i < polygon.size(); i++) {
			polygon.write[i] = polygon[i] * p_tile_set->get_tile_size();
		}
		add_polygon(polygon);
	}
	tile_set = p_tile_set;
	
	int default_control_y_size = 200 * EDSCALE;
	Vector2 zoomed_tile = editor_zoom_widget->get_zoom() * tile_set->get_tile_size();
	while (zoomed_tile.y < default_control_y_size) {
		editor_zoom_widget->set_zoom_by_increments(6, false);
		zoomed_tile = editor_zoom_widget->get_zoom() * tile_set->get_tile_size();
	}
	while (zoomed_tile.y > default_control_y_size) {
		editor_zoom_widget->set_zoom_by_increments(-6, false);
		zoomed_tile = editor_zoom_widget->get_zoom() * tile_set->get_tile_size();
	}
	editor_zoom_widget->set_zoom_by_increments(-6, false);
	_zoom_changed();
}
void GenericTilePolygonEditor::set_background(Ref<Texture2D> p_texture, Rect2 p_region, Vector2 p_offset, bool p_flip_h, bool p_flip_v, bool p_transpose, Color p_modulate) {