The author of the piece did due diligence in responding to all squawks from the peanut gallery except one, actually two posts on the same subject of how the "MIT data" is skewed because of how SWA structures profit sharing with pilots (apparently back heavy and applied to retirement plans with the airline) compared to the remaining big three US airlines. Why do you suppose that is?
The ASM comparison argument used by the author seems to be already decided to be also a little off, both there in the comments, and here.