### 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 (instantiated_scenes.is_empty()) {
		for (const KeyValue<Vector2i, String> &E : p_quadrant->scenes) {
			Node *node = tile_map_node->get_node_or_null(E.value);
			if (node) {
				node->queue_free();
			}
		}
		p_quadrant->scenes.clear();
	}
}
void TileMapLayer::_scenes_draw_quadrant_debug(TileMapQuadrant *p_quadrant) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	if (!Engine::get_singleton()->is_editor_hint()) {
		return;
	}
	
	RenderingServer *rs = RenderingServer::get_singleton();
	Vector2 quadrant_pos = tile_map_node->map_to_local(p_quadrant->coords * get_effective_quadrant_size());
	for (const Vector2i &E_cell : p_quadrant->cells) {
		const TileMapCell &c = get_cell(E_cell, true);
		TileSetSource *source;