### 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)
TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
									array.push_back(tile_data->is_valid_terrain_peering_bit(bit) ? tile_data->get_terrain_peering_bit(bit) : -1);
								}
								dict["terrain_peering_bits"] = array;
								drag_modified[cell] = dict;
								
								Rect2i texture_region = p_tile_atlas_view->get_alternative_tile_rect(coords, alternative_tile);
								Vector2i position = texture_region.get_center() + tile_data->get_texture_origin();
								Vector<Vector2> polygon = tile_set->get_terrain_polygon(terrain_set);
								if (Geometry2D::is_point_in_polygon(mb->get_position() - position, polygon)) {
									tile_data->set_terrain(terrain);
								}
								for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
									TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
									if (tile_set->is_valid_terrain_peering_bit(terrain_set, bit)) {
										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) {