This is a little speculative and I wasn't around for the original coining of the LW usage, but American geek slang has contained a much broader sense of "win" for quite a while. Someone conversant in that sociolect might say a project wins if it accomplishes its goals (related to but broader than sense 2 in the parent); they also might say an event is a win if it has some unexpected positive consequence, that a person wins if they display luck or excellence in some (not necessarily competitive) domain, et cetera. I'd expect that to have come from 1990s gamer jargon if you trace it back, but it's metastasized pretty far from those origins by now.

I'm guessing that "rationalists should win" derives from that usage.