I always view stopping power/effectivenss reports with a jaundiced eye. Typically, they are self-serving, either personally or professionally. The author even provides what amounts to a disclaimer for this very reason.
In general, I agree with the author. I have always been of the opinion that a hit with a .22 is much preferrable to a miss with a .44. Shot placement has always been, to my mind, far more important than caliber. Shoot someone in the eye with a .22 pistol. It may, or may not kill them outright but, I can assure you, either way they've lost all interest in the proceedings. Given that, any weapon that you can operate confidently, and shoot accurately is the one you should carry. Regardless of caliber.
After careful consideration, based on years of personal experience, I chose the .45 automatic. Specifically, I chose .45 in a 1911 platform. I shoot it well, the 1911 is just about as reliable as a machine can be, and the .45 delivers a substantial amount of energy to the target (I have begun trusting my XD quite a bit lately, but only after sending a considerable amount of lead downrange).
I will (and do) trust other pistols and calibers for personal protection. .357 magnum, .44 magnum, .41 magnum, and, oddly enough 5.7X28mm. I have personally seen what guns in these calibers can do when delivered properly.
However, having said allllll that... given the choice, like 'Flayer said, I prefer an AR with six spare mags and 100 yards (minimum) between me and the target.