### 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)
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 = p_value;
	tile_data->set_navigation_polygon(navigation_layer, nav_polygon);
	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());
}
Variant TileDataNavigationEditor::_get_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_V(tile_data, Variant());
	return tile_data->get_navigation_polygon(navigation_layer);
}
void TileDataNavigationEditor::_setup_undo_redo_action(TileSetAtlasSource *p_tile_set_atlas_source, HashMap<TileMapCell, Variant, TileMapCell> p_previous_values, Variant p_new_value) {
	EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
	for (const KeyValue<TileMapCell, Variant> &E : p_previous_values) {
		Vector2i coords = E.key.get_atlas_coords();
		undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/navigation_layer_%d/polygon", coords.x, coords.y, E.key.alternative_tile, navigation_layer), E.value);
		undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/navigation_layer_%d/polygon", coords.x, coords.y, E.key.alternative_tile, navigation_layer), p_new_value);
	}
}
void TileDataNavigationEditor::_tile_set_changed() {