### 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)

TILEMAP_CALL_FOR_LAYER_V(p_layer, TypedArray<Vector2i>(), get_used_cells_by_id);
}
Rect2i TileMap::get_used_rect() const {
	
	if (layers.is_empty()) {
		return Rect2i();
	}
	Rect2 rect = layers[0]->get_used_rect();
	for (unsigned int i = 1; i < layers.size(); i++) {
		rect = rect.merge(layers[i]->get_used_rect());
	}
	return rect;
}
void TileMap::set_light_mask(int p_light_mask) {
	
	CanvasItem::set_light_mask(p_light_mask);
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_light_mask_changed();
	}
}
void TileMap::set_material(const Ref<Material> &p_material) {
	
	CanvasItem::set_material(p_material);
	
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_material_changed();
	}
}
void TileMap::set_use_parent_material(bool p_use_parent_material) {