You could just use snapshots? You have to remember to revert to the previous snapshot after every use. You don't need to do that with disposables. And you can't run multiple instances, as you say.
Comments on How to use disposable VMs in GNOME Boxes (like Qubes, Windows Sandbox)
I agree that Boxes should have a persistent/transient toggle option. I think you've worked out the best option for people that just want to use Boxes. There's at least a dozen way to achieve this, including snapshots as Jon said, but most requires the use of command line programs.