### 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)

}
	if (!show_collision) {
		return;
	}
	RenderingServer *rs = RenderingServer::get_singleton();
	PhysicsServer2D *ps = PhysicsServer2D::get_singleton();
	Color debug_collision_color = tile_map_node->get_tree()->get_debug_collisions_color();
	Vector<Color> color;
	color.push_back(debug_collision_color);
	Vector2 quadrant_pos = tile_map_node->map_to_local(p_quadrant->coords * get_effective_quadrant_size());
	Transform2D quadrant_to_local;
	quadrant_to_local.set_origin(quadrant_pos);
	Transform2D global_to_quadrant = (tile_map_node->get_global_transform() * quadrant_to_local).affine_inverse();
	for (RID body : p_quadrant->bodies) {
		Transform2D body_to_quadrant = global_to_quadrant * Transform2D(ps->body_get_state(body, PhysicsServer2D::BODY_STATE_TRANSFORM));
		rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, body_to_quadrant);
		for (int shape_index = 0; shape_index < ps->body_get_shape_count(body); shape_index++) {
			const RID &shape = ps->body_get_shape(body, shape_index);
			PhysicsServer2D::ShapeType type = ps->shape_get_type(shape);
			if (type == PhysicsServer2D::SHAPE_CONVEX_POLYGON) {
				Vector<Vector2> polygon = ps->shape_get_data(shape);
				rs->canvas_item_add_polygon(p_quadrant->debug_canvas_item, polygon, color);
			} else {
				WARN_PRINT("Wrong shape type for a tile, should be SHAPE_CONVEX_POLYGON.");
			}
		}
		rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, Transform2D());
	}
};
void TileMapLayer::_navigation_update_dirty_quadrants(SelfList<TileMapQuadrant>::List &r_dirty_quadrant_list) {