### 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 (_tile_set_changed_deferred_update_needed) {
		_clear_internals();
		_recreate_internals();
		_tile_set_changed_deferred_update_needed = false;
	}
}
TileMap::TileMap() {
	set_notify_transform(true);
	set_notify_local_transform(false);
	Ref<TileMapLayer> new_layer;
	new_layer.instantiate();
	new_layer->set_tile_map(this);
	new_layer->set_layer_index_in_tile_map_node(0);
	layers.push_back(new_layer);
}
TileMap::~TileMap() {
	if (tile_set.is_valid()) {
		tile_set->disconnect_changed(callable_mp(this, &TileMap::_tile_set_changed));
	}
	_clear_internals();
}
#undef TILEMAP_CALL_FOR_LAYER
#undef TILEMAP_CALL_FOR_LAYER_V