I think with Flake, it's a lot more complicated. He's always been a slippery henchman, not a "boss." Flake, honestly, is not very smart. Well, he's the kind of guy who has certain talents and just enough smarts to get him into troubleโฆ Which definately happened. Now he has to leave politics.
I think its very clear that POTUS and Q have left his ultimate fate unclear. He's half hoping that he can just slink away and fade into the background. At the same time, he has to hedge his bets.
Long story short, Flake is part cuck, part tool and part Peter Lorre in The Maltese Falcon.