### 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)
base_control->queue_redraw();
}
void GenericTilePolygonEditor::_advanced_menu_item_pressed(int p_item_pressed) {
	EditorUndoRedoManager *undo_redo;
	if (use_undo_redo) {
		undo_redo = EditorUndoRedoManager::get_singleton();
	} else {
		
		undo_redo = memnew(EditorUndoRedoManager);
	}
	switch (p_item_pressed) {
		case RESET_TO_DEFAULT_TILE: {
			undo_redo->create_action(TTR("Reset Polygons"));
			undo_redo->add_do_method(this, "clear_polygons");
			Vector<Vector2> polygon = tile_set->get_tile_shape_polygon();
			for (int i = 0; i < polygon.size(); i++) {
				polygon.write[i] = polygon[i] * tile_set->get_tile_size();
			}
			undo_redo->add_do_method(this, "add_polygon", polygon);
			undo_redo->add_do_method(base_control, "queue_redraw");
			undo_redo->add_do_method(this, "emit_signal", "polygons_changed");
			undo_redo->add_undo_method(this, "clear_polygons");
			for (const PackedVector2Array &poly : polygons) {
				undo_redo->add_undo_method(this, "add_polygon", poly);
			}
			undo_redo->add_undo_method(base_control, "queue_redraw");
			undo_redo->add_undo_method(this, "emit_signal", "polygons_changed");
			undo_redo->commit_action(true);
		} break;
		case CLEAR_TILE: {