1. The "error" you refer to isn't really an obvious one at all. That is, delta efficiency has been/can be calculated various ways in different papers, with the method that Coyle actually used being an acceptable one. The only real mistake was in citing the wrong paper, i.e., one that did take into account changes in the intercept, as is sometimes, but not always, done.
2. I agree that the paper in question wouldn't have gotten published if Armstrong hadn't been the subject, and Ashenden likely wouldn't have gotten all worked up about it if it hadn't been for the SCA lawsuit. Be that as it may, though, I think it is quite telling that the general observation - i.e., that cycling efficiency tends to improve over time in those who train at a very high level for many years - has now been confirmed in a couple of subsequent studies (with multiple subjects, not just one).
Anyway, as for responding to Ross and Jon, I actually posted quite a few times to their blog, but all but one of my posts has now been removed...