No doubt GPUs have the advantage, even one 1080 has way more hashpower than most CPUs, not to mention you can have bunch of them in one rig, while multi-processor systems are only on high end servers. Although Webchain officially don't support GPU mining and altered the algo to even the level, community are doing it anyway.
Nobody will stop them from doing it. That's the beauty of decentralized system.
What JSE is doing instead is complete and total centralization, and they admit to it, let me quote them "The JSEcoin system is currently fully centralized. " taken from their page.
So the question is why they do mining at all? It's artificial mining that has no use case.
Normally mining is there to secure decentralized network. In centralized system like that, it makes absolutely no sense. They kept it as marketing trick I guess so people who earlier mined decentralized coins can switch and feel like at home, thinking they are doing same thing. But they don't.
Good luck with that aproach long-term.