I don't quite get the confusion.

Observing that people are likelier to experience Y upon getting X than people who don't get X (which, incidentally, is more than just "X is strongly correlated with Y," which is a weaker claim) is evidence that X reliably entails Y.

It is not evidence for any particular mechanism underlying that entailment (since it's equally compatible with a great many mechanisms).

So I'd be justified, based on a novel study that showed that, in increasing my estimate of the probability of Y given X, though I shouldn't increase my estimate of the probability of any particular mechanism.

The fact that the mechanism in this case is a bias pervasive within the group doesn't change any of that.