### 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("get_used_rect"), &TileMap::get_used_rect);
	ClassDB::bind_method(D_METHOD("map_to_local", "map_position"), &TileMap::map_to_local);
	ClassDB::bind_method(D_METHOD("local_to_map", "local_position"), &TileMap::local_to_map);
	ClassDB::bind_method(D_METHOD("get_neighbor_cell", "coords", "neighbor"), &TileMap::get_neighbor_cell);
	ClassDB::bind_method(D_METHOD("_update_dirty_quadrants"), &TileMap::_update_dirty_quadrants);
	ClassDB::bind_method(D_METHOD("_tile_set_changed_deferred_update"), &TileMap::_tile_set_changed_deferred_update);
	GDVIRTUAL_BIND(_use_tile_data_runtime_update, "layer", "coords");
	GDVIRTUAL_BIND(_tile_data_runtime_update, "layer", "coords", "tile_data");
	ADD_PROPERTY(PropertyInfo(Variant::OBJECT, "tile_set", PROPERTY_HINT_RESOURCE_TYPE, "TileSet"), "set_tileset", "get_tileset");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "cell_quadrant_size", PROPERTY_HINT_RANGE, "1,128,1"), "set_quadrant_size", "get_quadrant_size");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "collision_animatable"), "set_collision_animatable", "is_collision_animatable");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "collision_visibility_mode", PROPERTY_HINT_ENUM, "Default,Force Show,Force Hide"), "set_collision_visibility_mode", "get_collision_visibility_mode");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "navigation_visibility_mode", PROPERTY_HINT_ENUM, "Default,Force Show,Force Hide"), "set_navigation_visibility_mode", "get_navigation_visibility_mode");
	ADD_ARRAY("layers", "layer_");
	ADD_PROPERTY_DEFAULT("format", TileMapLayer::FORMAT_1);
	ADD_SIGNAL(MethodInfo(CoreStringNames::get_singleton()->changed));
	BIND_ENUM_CONSTANT(VISIBILITY_MODE_DEFAULT);
	BIND_ENUM_CONSTANT(VISIBILITY_MODE_FORCE_HIDE);
	BIND_ENUM_CONSTANT(VISIBILITY_MODE_FORCE_SHOW);
}
void TileMap::_tile_set_changed() {
	emit_signal(CoreStringNames::get_singleton()->changed);
	_tile_set_changed_deferred_update_needed = true;
	for (Ref<TileMapLayer> &layer : layers) {
		layer->clear_instantiated_scenes();
	}
	call_deferred(SNAME("_tile_set_changed_deferred_update"));
	update_configuration_warnings();
}
void TileMap::_tile_set_changed_deferred_update() {