### 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_INDEX(p_layer, (int)layers.size());
	ERR_FAIL_INDEX(p_to_pos, (int)layers.size() + 1);
	
	_clear_internals();
	Ref<TileMapLayer> layer = layers[p_layer];
	layers.insert(p_to_pos, layer);
	layers.remove_at(p_to_pos < p_layer ? p_layer + 1 : p_layer);
	for (unsigned int i = 0; i < layers.size(); i++) {
		layers[i]->set_layer_index_in_tile_map_node(i);
	}
	_recreate_internals();
	notify_property_list_changed();
	if (selected_layer == p_layer) {
		selected_layer = p_to_pos < p_layer ? p_to_pos - 1 : p_to_pos;
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
	update_configuration_warnings();
}
void TileMap::remove_layer(int p_layer) {