Ads, until the introduction of iAds, would not have gone through apple, and therefor would not count towards total revenue.

You do have a point with in app purchases, but I doubt that they would significantly skew the numbers - they would make them worse for developers of paid apps, in fact. Given the other optimistic decisions the article has when dealing with numbers, I think that ignoring in app purchases fits with it: it's a best case scenario for paid apps.

It would be quite interesting to see how much money has been made through in app purchases, though. Not merely anecdotes, but the percentage of free apps which have in app purchases, and the average/median income through in app purchases in those apps.