Yeah, that's an artefact of the way banners work and the fact that they were once on-topic. The short answer is that flagging and close votes is the only way to deal with it effectively.
The long answer is that banners are manually added or removed. (So fortunately, no new banners are going to happen.) The mods could go on a purging binge and remove banners while closing all the things, but that's a lot of work for minimal payoff. In practice what we've been doing is handling them organically: dealing with them as they get bumped, turn up in searches, turn up in comment or post flags, or get closed by five votes (which bumps them). Basically, when we notice them we deal with them. Dealing with them means closing them if that still needs doing and/or (preferably both) tossing a Historical Lock on them so that they stop getting bumped.
But we've been leaving the banners on. As contradictory as it seems, it doesn't make sense to remove the banners once it's got the Historical Lock's banner beside it. The old game-rec banner serves a useful purpose in directing people to the metas where it was explained how they used to be on-topic, even while the more recently-dated close notice points to the later meta explaining why they aren't anymore, and the Historical Lock's banner says these used to be considered good, on-topic questions but aren't anymore. The questions end up looking like this.
Leaving the game-rec banner on a game-rec question that we've dealt with is helpful because it provides all the context necessary to a curious reader. And game-rec banners on questions that we haven't noticed and processed can't be removed because by definition we haven't seen and processed those questions yet.
One thing that can be helped though, and I've just done an edit to do so: the game-rec banner leads directly to this answer in our old game-rec policy meta. Though the meta Q itself has a duplicate banner clearly pointing to the new guidance (“sadly they are off topic”), the direct link to that answer makes it easy for curious readers to never see the link, and instead read a pageful of answer saying that they are on topic. Oops. To fix that I've added a pseudo-banner at the top of the answer saying it's historical and overturned, with a link to the new guidance.
So thank you! I think that's an improvement.
But the short of it is, again: flag 'em when you see 'em, so we can throw closes and locks on them, along with their attendant banners that explain all this more directly.