### 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)

Color debug_edge_color = ns2d->get_debug_navigation_geometry_edge_color();
	RandomPCG rand;
	Vector2 quadrant_pos = tile_map_node->map_to_local(p_quadrant->coords * get_effective_quadrant_size());
	for (const Vector2i &E_cell : p_quadrant->cells) {
		TileMapCell c = get_cell(E_cell, true);
		TileSetSource *source;
		if (tile_set->has_source(c.source_id)) {
			source = *tile_set->get_source(c.source_id);
			if (!source->has_tile(c.get_atlas_coords()) || !source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
				continue;
			}
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				const TileData *tile_data;
				if (p_quadrant->runtime_tile_data_cache.has(E_cell)) {
					tile_data = p_quadrant->runtime_tile_data_cache[E_cell];
				} else {
					tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
				}
				Transform2D cell_to_quadrant;
				cell_to_quadrant.set_origin(tile_map_node->map_to_local(E_cell) - quadrant_pos);
				rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, cell_to_quadrant);
				for (int layer_index = 0; layer_index < tile_set->get_navigation_layers_count(); layer_index++) {
					Ref<NavigationPolygon> navigation_polygon = tile_data->get_navigation_polygon(layer_index);
					if (navigation_polygon.is_valid()) {
						Vector<Vector2> navigation_polygon_vertices = navigation_polygon->get_vertices();
						if (navigation_polygon_vertices.size() < 3) {
							continue;
						}
						for (int i = 0; i < navigation_polygon->get_polygon_count(); i++) {