### 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)

ERR_FAIL_COND(!tile_map_node->is_inside_tree());
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	Transform2D tilemap_xform = tile_map_node->get_global_transform();
	SelfList<TileMapQuadrant> *q_list_element = r_dirty_quadrant_list.first();
	while (q_list_element) {
		TileMapQuadrant &q = *q_list_element->self();
		
		for (const KeyValue<Vector2i, Vector<RID>> &E : q.navigation_regions) {
			for (int i = 0; i < E.value.size(); i++) {
				RID region = E.value[i];
				if (!region.is_valid()) {
					continue;
				}
				NavigationServer2D::get_singleton()->region_set_map(region, RID());
			}
		}
		q.navigation_regions.clear();
		
		for (const Vector2i &E_cell : q.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);