You misunderstand: The plaintif's argument is that you are
only protected from the patent if the software is distributed
via the GPL. Since Versata's customers
did NOT get the software under the terms of the GPL, they
are not protected by the GPL license that Versata refused to abide by The alternative was to pay for a commercial patent license, but nobody bothered to do that, either.
Thus, both Versata and their customers are in the legal dog house.
Technically, Ximpleware doesn't even have to raise the GPL. All that they have to do is sue Versata and their customers for copyright and patent violations. If either tries to claim the GPL as a defense, then the response to that claim is that the GPL doesn't apply to this case because Versata didn't even try to abide by the terms of the GPL.
The code wasn't distributed for free. It was distributed under a choice of two separate licenses: One was the GPL, one was commercial. Clearly, the commercial license route wasn't taken, and the GPL license wasn't adhered to.
Irrelevant if the patent owners argument is accepted that the GPL license did not include a license to use the software because you also needed to obtain a license for the patent that the GPL'd source uses. It's like cops putting out a plate of free 'special' (unmarked as such) brownies next to a plate of $5-per regular brownies at back-to-school night and promptly arresting everybody who eats one of the 'free' brownies.
If Oracle pulled such a BS claim out in their Java lawsuits, everybody but the corporate lawyers would be puking in disgust at such a bold admission of intent to entrap users.