Even if the publisher requested it, BGA agreed to that and introduced a workaround/backdoor. I think BGA should have some basic principles publishers must accept regarding how the platform works and what is and isn't allowed. And I believe "equal treatment of all players" should be one of them.
But, on second thought, I believe this is not the first time it happens. If I'm not mistaken, Altered allows you to buy cards and customize your deck, which ends up with the same result: different players getting different in-game opportunities. The difference is that this is not linked to BGA premium status. I would be more comfortable if the premium factions were linked to some account/subscription outside BGA.