Odds are, he will one-box, especially if the punishment for correctly predicted two-boxing is harsh enough.

This isn't an argument (at least not a direct argument) that one-boxing is more rational. Two-boxers grant that one-boxing gets you more money. They just say that sometimes, a situation might arise that punishes rational decision making. And they may well agree that in such a situation, they would one box irrationally. The question isn't 'what would you do?', the question is 'what is it rational to do?'

You might reply that what's rational is just what gets you the most money, but that's precisely the point that's up for dispute. If you assume that rationality is just whatever makes you richer, you beg the question.