Indeed, the persist behavior doesn't seem to have been thought for the "reset" case.
That's something Ashley might want to have a look on, to add a way to reset a game that uses Persist behaviors.
In the absolute, I think the persist behavior wasn't really intended to be used in such games since its point is to remember the state of the objects, so you are expecting a persistent world, not necessary a world you would reset/start from scratch all over again.
Global property set to "Yes" just makes that the instances don't get destroyed when moving from a layout to another. The object that is set to global also stays at the same position when changing the layout.
So it does not sit well with the persist behavior anyway.