### 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)

}
	
	_build_runtime_update_tile_data(dirty_quadrant_list);
	
	_rendering_update_dirty_quadrants(dirty_quadrant_list);
	_physics_update_dirty_quadrants(dirty_quadrant_list);
	_navigation_update_dirty_quadrants(dirty_quadrant_list);
	_scenes_update_dirty_quadrants(dirty_quadrant_list);
	
	RenderingServer *rs = RenderingServer::get_singleton();
	for (SelfList<TileMapQuadrant> *q = dirty_quadrant_list.first(); q; q = q->next()) {
		rs->canvas_item_clear(q->self()->debug_canvas_item);
		Transform2D xform;
		xform.set_origin(tile_map_node->map_to_local(q->self()->coords * get_effective_quadrant_size()));
		rs->canvas_item_set_transform(q->self()->debug_canvas_item, xform);
		_rendering_draw_quadrant_debug(q->self());
		_physics_draw_quadrant_debug(q->self());
		_navigation_draw_quadrant_debug(q->self());
		_scenes_draw_quadrant_debug(q->self());
	}
	
	while (dirty_quadrant_list.first()) {
		
		for (const KeyValue<Vector2i, TileData *> &kv : dirty_quadrant_list.first()->self()->runtime_tile_data_cache) {
			memdelete(kv.value);
		}
		dirty_quadrant_list.remove(dirty_quadrant_list.first());
	}
}
void TileMapLayer::set_cell(const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {