The simple way to think about R^2 is that it is a measure of relative predictive accuracy (and that is exactly how it is calculated). This is both a more accurate (and a more useful definition for most tasks the HN crowd would work on) than saying R^2 is a measure of the distance from the true model.
All the figures and findings in the post are completely reasonable given that definition (the linear model performing better in the first case is due to the high variance of the author's data, other samplings would lead to the reverse result).