### 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)
Ref<NavigationPolygon> nav_polygon;
	nav_polygon.instantiate();
	if (polygon_editor->get_polygon_count() > 0) {
		Ref<NavigationMeshSourceGeometryData2D> source_geometry_data;
		source_geometry_data.instantiate();
		for (int i = 0; i < polygon_editor->get_polygon_count(); i++) {
			Vector<Vector2> polygon = polygon_editor->get_polygon(i);
			nav_polygon->add_outline(polygon);
			source_geometry_data->add_traversable_outline(polygon);
		}
		nav_polygon->set_agent_radius(0.0);
		NavigationServer2D::get_singleton()->bake_from_source_geometry_data(nav_polygon, source_geometry_data);
	} else {
		nav_polygon->clear();
	}
	return nav_polygon;
}
void TileDataNavigationEditor::_set_painted_value(TileSetAtlasSource *p_tile_set_atlas_source, Vector2 p_coords, int p_alternative_tile) {
	TileData *tile_data = p_tile_set_atlas_source->get_tile_data(p_coords, p_alternative_tile);
	ERR_FAIL_NULL(tile_data);
	Ref<NavigationPolygon> nav_polygon = tile_data->get_navigation_polygon(navigation_layer);
	polygon_editor->clear_polygons();
	if (nav_polygon.is_valid()) {
		for (int i = 0; i < nav_polygon->get_outline_count(); i++) {
			polygon_editor->add_polygon(nav_polygon->get_outline(i));
		}
	}
	polygon_editor->set_background(p_tile_set_atlas_source->get_texture(), p_tile_set_atlas_source->get_tile_texture_region(p_coords), tile_data->get_texture_origin(), tile_data->get_flip_h(), tile_data->get_flip_v(), tile_data->get_transpose(), tile_data->get_modulate());
}
void TileDataNavigationEditor::_set_value(TileSetAtlasSource *p_tile_set_atlas_source, Vector2 p_coords, int p_alternative_tile, Variant p_value) {