You're reading this uncharitably. There are also parts that are unclear on Yvain's part, sure, but not to the extent that you claim.

The original group project situation Yvain explores does mirror the Prisoner's Dilemma. Then, later, he introduces reputational effects to illustrate one of the Real World Solutions to the Prisoner's Dilemma that we have already developed.

It's not made crystal clear....

So one might expect the real world to have produced some practical solutions to Prisoners' Dilemmas. One of the best known such systems is called “society”. You may have heard of it.

Well, actually it is.

...

Evolution

I understood Yvain to be speaking metaphorically, or perhaps tongue-in-cheek, when talking about what evolution would take note of. I believe this was his intention, and furthermore is a reasonable reading given our knowledge of Yvain.

This is in direct violation of one of the themes of Less Wrong. If "rational expected utility maximizers" are doing worse than "irrational emotional hangups", then you're using a wrong definition of "rational". You do this throughout the post, and it's especially jarring because you are or were one of the best writers for this website.

I expect that Yvain used 'rational' against the theme of LW on purpose, to create a tension - rationality failing to outperform emotional hangups is a contradiction, that would motivate readers to find the false premise or re-analyse the situation.

I do concur with your point about tit-for-tat. Similarly for super-rationality; although it's possible Yvain is not familiar with Hofstadter's definition and was using 'super' as an intensifier, it seems unlikely.