### 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)
if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
						TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, 0);
						int terrain_set = tile_data->get_terrain_set();
						Rect2i texture_region = p_tile_set_atlas_source->get_tile_texture_region(coords);
						Vector2i position = texture_region.get_center() + tile_data->get_texture_origin();
						dummy_object->set("terrain_set", terrain_set);
						dummy_object->set("terrain", -1);
						Vector<Vector2> polygon = tile_set->get_terrain_polygon(terrain_set);
						if (Geometry2D::is_point_in_polygon(mb->get_position() - position, polygon)) {
							dummy_object->set("terrain", tile_data->get_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)) {
									dummy_object->set("terrain", tile_data->get_terrain_peering_bit(bit));
								}
							}
						}
						terrain_set_property_editor->update_property();
						_update_terrain_selector();
						picker_button->set_pressed(false);
						accept_event();
					}
				} else {
					Vector2i coords = p_tile_atlas_view->get_atlas_tile_coords_at_pos(mb->get_position());
					coords = p_tile_set_atlas_source->get_tile_at_coords(coords);
					TileData *tile_data = nullptr;
					if (coords != TileSetAtlasSource::INVALID_ATLAS_COORDS) {