### 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_NULL(PhysicsServer2D::get_singleton());
	for (RID body : p_quadrant->bodies) {
		bodies_coords.erase(body);
		PhysicsServer2D::get_singleton()->free(body);
	}
	p_quadrant->bodies.clear();
}
void TileMapLayer::_physics_draw_quadrant_debug(TileMapQuadrant *p_quadrant) {
	
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	if (!tile_map_node->get_tree()) {
		return;
	}
	bool show_collision = false;
	switch (tile_map_node->get_collision_visibility_mode()) {
		case TileMap::VISIBILITY_MODE_DEFAULT:
			show_collision = !Engine::get_singleton()->is_editor_hint() && tile_map_node->get_tree()->is_debugging_collisions_hint();
			break;
		case TileMap::VISIBILITY_MODE_FORCE_HIDE:
			show_collision = false;
			break;
		case TileMap::VISIBILITY_MODE_FORCE_SHOW:
			show_collision = true;
			break;