### 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)

const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (!tile_set.is_valid()) {
		return HashMap<Vector2i, TileSet::TerrainsPattern>();
	}
	
	RBSet<TerrainConstraint> constraints = p_constraints;
	
	HashMap<Vector2i, TileSet::TerrainsPattern> output;
	
	for (int i = 0; i < p_to_replace.size(); i++) {
		const Vector2i &coords = p_to_replace[i];
		
		TileSet::TerrainsPattern current_pattern = TileSet::TerrainsPattern(*tile_set, p_terrain_set);
		TileMapCell cell = get_cell(coords);
		if (cell.source_id != TileSet::INVALID_SOURCE) {
			TileSetSource *source = *tile_set->get_source(cell.source_id);
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {