The analytic result (that only 2 of 736 strategically unique ordinal 2×2 games are PDs) is interesting, the numerical simulation less so; the paper doesn't motivate the specific choice of a uniform distribution from which to randomly sample payoffs. (I can imagine the results changing quite a lot if the payoffs are taken from e.g. lognormal or normal distributions instead.)
Wanna bet? I made a few Prediction Book entries. The author was nice enough to give me his source code; I modified it and ran it. I will edit this comment as soon as I finish cranking out the results. I'll rot13 them, or hide them in a spoiler window (is that possible?), for those who'd like to try a Prediction Book probability estimate.
I neglected to make Prediction Book entries for the lognormal distribution, but they would have been similar. Herewith, the results in rot13:
Normal distribution: guerr cbvag sbhe creprag
Lognormal: guerr cbvag svir cre...
Hannes Rusch argues that the Prisoner's Dilemma is best understood as merely one game of very many:
http://www2.units.it/etica/2013_2/RUSCH.pdf