I read the article, but I'll admit I only skimmed it. However, the thing that sticks out to me is his methodology. Why does he use the whole BCS era? No one, at least no one with any college-football knowledge whatsoever, will claim that the SEC was the dominant conference in the late 90s/early 00s. Yes, there were some great teams, but the SEC dominance is a relatively new phenomenon. Let's not forget that Auburn was left out of the 2004 NC game despite being undefeated, and Georgia missed it in 2002 despite having only lost to ranked Florida. The whole "SEC RULES!!!" thing really got rolling somewhere around 2006-07 and then just fed into itself.
Let's also not forget that the SEC doesn't get particularly favorable bowl match-ups outside of the BCS because it generally sends two teams to BCS bowls.
So, yeah, one can argue that the SEC hasn't been dominant for 15 years, but you're not going to be arguing against anyone, since that's not what SEC fans assert. We assert that the SEC has been dominant over the last half decade or so (really a little more), and the numbers bear that out.
For the record, I will say that the whole Bama rematch thing was complete horseshit, and no one outside of Tuscaloosa thinks it was right. In addition, I'm sure the SEC gets a little bit over-credited in the rankings because of past performance, but that's just the nature of the system.