### 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)

Ref<TileMapLayer> new_layer;
				new_layer.instantiate();
				new_layer->set_tile_map(this);
				new_layer->set_layer_index_in_tile_map_node(index);
				layers.push_back(new_layer);
			}
			_recreate_internals();
			notify_property_list_changed();
			emit_signal(CoreStringNames::get_singleton()->changed);
			update_configuration_warnings();
		}
		if (components[1] == "name") {
			set_layer_name(index, p_value);
			return true;
		} else if (components[1] == "enabled") {
			set_layer_enabled(index, p_value);
			return true;
		} else if (components[1] == "modulate") {
			set_layer_modulate(index, p_value);
			return true;
		} else if (components[1] == "y_sort_enabled") {
			set_layer_y_sort_enabled(index, p_value);
			return true;
		} else if (components[1] == "y_sort_origin") {
			set_layer_y_sort_origin(index, p_value);
			return true;
		} else if (components[1] == "z_index") {
			set_layer_z_index(index, p_value);
			return true;
		} else if (components[1] == "tile_data") {