### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_BOUNCE, 0);
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_FRICTION, 1);
						} else {
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_BOUNCE, physics_material->computed_bounce());
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_FRICTION, physics_material->computed_friction());
						}
						q.bodies.push_back(body);
						
						int body_shape_index = 0;
						for (int polygon_index = 0; polygon_index < tile_data->get_collision_polygons_count(tile_set_physics_layer); polygon_index++) {
							
							bool one_way_collision = tile_data->is_collision_polygon_one_way(tile_set_physics_layer, polygon_index);
							float one_way_collision_margin = tile_data->get_collision_polygon_one_way_margin(tile_set_physics_layer, polygon_index);
							int shapes_count = tile_data->get_collision_polygon_shapes_count(tile_set_physics_layer, polygon_index);
							for (int shape_index = 0; shape_index < shapes_count; shape_index++) {
								
								Ref<ConvexPolygonShape2D> shape = tile_data->get_collision_polygon_shape(tile_set_physics_layer, polygon_index, shape_index);
								ps->body_add_shape(body, shape->get_rid());
								ps->body_set_shape_as_one_way_collision(body, body_shape_index, one_way_collision, one_way_collision_margin);
								body_shape_index++;
							}
						}
					}
				}
			}
		}
		q_list_element = q_list_element->next();
	}
}
void TileMapLayer::_physics_cleanup_quadrant(TileMapQuadrant *p_quadrant) {