Neptune does have a new module for controlling the Vortech's but it's only compatible with the Apex line, not a Jr. Even with that I don't think the interface ever really stops the pump, just slows it down and speeds it up depending on the profile selected.
So the question remains... should you turn it on and off for extended periods... I wouldn't with mine, basically because of the fall off principal and none of their profiles do it. Mine always starts rough and slips a little when it's off for any reason ( MP10) so I would be worried that it would fall and just not work. That being said I'd be interested in what Vortech says......
Dave