### 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)

ClassDB::bind_method(D_METHOD("set_tileset", "tileset"), &TileMap::set_tileset);
	ClassDB::bind_method(D_METHOD("get_tileset"), &TileMap::get_tileset);
	ClassDB::bind_method(D_METHOD("set_quadrant_size", "size"), &TileMap::set_quadrant_size);
	ClassDB::bind_method(D_METHOD("get_quadrant_size"), &TileMap::get_quadrant_size);
	ClassDB::bind_method(D_METHOD("get_layers_count"), &TileMap::get_layers_count);
	ClassDB::bind_method(D_METHOD("add_layer", "to_position"), &TileMap::add_layer);
	ClassDB::bind_method(D_METHOD("move_layer", "layer", "to_position"), &TileMap::move_layer);
	ClassDB::bind_method(D_METHOD("remove_layer", "layer"), &TileMap::remove_layer);
	ClassDB::bind_method(D_METHOD("set_layer_name", "layer", "name"), &TileMap::set_layer_name);
	ClassDB::bind_method(D_METHOD("get_layer_name", "layer"), &TileMap::get_layer_name);
	ClassDB::bind_method(D_METHOD("set_layer_enabled", "layer", "enabled"), &TileMap::set_layer_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_enabled", "layer"), &TileMap::is_layer_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_modulate", "layer", "modulate"), &TileMap::set_layer_modulate);
	ClassDB::bind_method(D_METHOD("get_layer_modulate", "layer"), &TileMap::get_layer_modulate);
	ClassDB::bind_method(D_METHOD("set_layer_y_sort_enabled", "layer", "y_sort_enabled"), &TileMap::set_layer_y_sort_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_y_sort_enabled", "layer"), &TileMap::is_layer_y_sort_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_y_sort_origin", "layer", "y_sort_origin"), &TileMap::set_layer_y_sort_origin);
	ClassDB::bind_method(D_METHOD("get_layer_y_sort_origin", "layer"), &TileMap::get_layer_y_sort_origin);
	ClassDB::bind_method(D_METHOD("set_layer_z_index", "layer", "z_index"), &TileMap::set_layer_z_index);
	ClassDB::bind_method(D_METHOD("get_layer_z_index", "layer"), &TileMap::get_layer_z_index);
	ClassDB::bind_method(D_METHOD("set_layer_navigation_map", "layer", "map"), &TileMap::set_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("get_layer_navigation_map", "layer"), &TileMap::get_layer_navigation_map);