### 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)
current_snap_option = p_index;
	button_pixel_snap->set_icon(button_pixel_snap->get_popup()->get_item_icon(p_index));
	snap_subdivision->set_visible(p_index == SNAP_GRID);
	base_control->queue_redraw();
	_store_snap_options();
}
void GenericTilePolygonEditor::_store_snap_options() {
	EditorSettings::get_singleton()->set_project_metadata("editor_metadata", "tile_snap_option", current_snap_option);
	EditorSettings::get_singleton()->set_project_metadata("editor_metadata", "tile_snap_subdiv", snap_subdivision->get_value());
}
void GenericTilePolygonEditor::_toggle_expand(bool p_expand) {
	if (p_expand) {
		TileSetEditor::get_singleton()->add_expanded_editor(this);
	} else {
		TileSetEditor::get_singleton()->remove_expanded_editor();
	}
}
void GenericTilePolygonEditor::set_use_undo_redo(bool p_use_undo_redo) {
	use_undo_redo = p_use_undo_redo;
}
void GenericTilePolygonEditor::set_tile_set(Ref<TileSet> p_tile_set) {