### 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)
r_current_snapped_dist = distance;
			}
		}
	}
	r_point = snapped_point;
}
void GenericTilePolygonEditor::_snap_point(Point2 &r_point) {
	switch (current_snap_option) {
		case SNAP_NONE:
			break;
		case SNAP_HALF_PIXEL:
			r_point = r_point.snapped(Vector2(0.5, 0.5));
			break;
		case SNAP_GRID: {
			const Vector2 tile_size = tile_set->get_tile_size();
			r_point = (r_point + tile_size / 2).snapped(tile_size / snap_subdivision->get_value()) - tile_size / 2;
		} break;
	}
}
void GenericTilePolygonEditor::_base_control_gui_input(Ref<InputEvent> p_event) {
	EditorUndoRedoManager *undo_redo;
	if (use_undo_redo) {
		undo_redo = EditorUndoRedoManager::get_singleton();
	} else {
		
		undo_redo = memnew(EditorUndoRedoManager);
	}
	real_t grab_threshold = EDITOR_GET("editors/polygon_editor/point_grab_radius");
	hovered_polygon_index = -1;
	hovered_point_index = -1;