### 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)
polygon = tile_set->get_terrain_peering_bit_polygon(terrain_set, bit);
										if (Geometry2D::is_point_in_polygon(mb->get_position() - position, polygon)) {
											tile_data->set_terrain_peering_bit(bit, terrain);
										}
									}
								}
							}
							drag_last_pos = mb->get_position();
						}
						accept_event();
					}
				}
			} else {
				EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
				if (drag_type == DRAG_TYPE_PAINT_TERRAIN_SET_RECT) {
					Rect2i rect;
					rect.set_position(p_tile_atlas_view->get_atlas_tile_coords_at_pos(drag_start_pos, true));
					rect.set_end(p_tile_atlas_view->get_atlas_tile_coords_at_pos(mb->get_position(), true));
					rect = rect.abs();
					RBSet<TileMapCell> edited;
					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;
								edited.insert(cell);