### 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)
rect = rect.abs();
					drag_modified.clear();
					for (int x = rect.get_position().x; x <= rect.get_end().x; x++) {
						for (int y = rect.get_position().y; y <= rect.get_end().y; y++) {
							Vector2i coords = Vector2i(x, y);
							coords = p_tile_set_atlas_source->get_tile_at_coords(coords);
							if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
								TileMapCell cell;
								cell.source_id = 0;
								cell.set_atlas_coords(coords);
								cell.alternative_tile = 0;
								drag_modified[cell] = _get_value(p_tile_set_atlas_source, coords, 0);
							}
						}
					}
					undo_redo->create_action(TTR("Painting Tiles Property"));
					_setup_undo_redo_action(p_tile_set_atlas_source, drag_modified, drag_painted_value);
					undo_redo->commit_action(true);
					drag_type = DRAG_TYPE_NONE;
				} else if (drag_type == DRAG_TYPE_PAINT) {
					undo_redo->create_action(TTR("Painting Tiles Property"));
					_setup_undo_redo_action(p_tile_set_atlas_source, drag_modified, drag_painted_value);
					undo_redo->commit_action(false);
					drag_type = DRAG_TYPE_NONE;
				}
			}
		}
	}
}
void TileDataDefaultEditor::forward_painting_alternatives_gui_input(TileAtlasView *p_tile_atlas_view, TileSetAtlasSource *p_tile_set_atlas_source, const Ref<InputEvent> &p_event) {