### 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)
undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/terrains_peering_bit/" + String(TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[i]), coords.x, coords.y, E.key.alternative_tile), array[i]);
							}
						}
					}
					undo_redo->commit_action(false);
					drag_type = DRAG_TYPE_NONE;
					accept_event();
				} else if (drag_type == DRAG_TYPE_PAINT_TERRAIN_BITS_RECT) {
					Dictionary painted = Dictionary(drag_painted_value);
					int terrain_set = int(painted["terrain_set"]);
					int terrain = int(painted["terrain"]);
					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) {
								TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, 0);
								if (tile_data->get_terrain_set() == terrain_set) {
									TileMapCell cell;
									cell.source_id = 0;
									cell.set_atlas_coords(coords);
									cell.alternative_tile = 0;
									edited.insert(cell);
								}
							}