To be honest, most of BB's customers aren't buying the top of the line displays, aren't buying any projectors, etc etc. Going to the nines with CMS isn't something I think someone would naturally expect from BB. Even if equipped and trained to deal with CMS, the opportunity to even calibrate a display with CMS is not the most common these days (though admittedly this is changing). The extra time is also significant. CMS is covered very briefly in BB's training, and to be honest I think that's fine. Unleashing briefly-trained techs on CMS systems can waste a lot of time and end up with chaos while calibrating if you don't have a really good grasp of what's going on and what you're doing.
I think it's also fair to point out that we here at AVS have something of a bias because many of the most knowledgeable and experienced calibrators frequent this forum, but keep in mind that the vast majority of ISF techs out there (not including Best Buy) are not up to this caliber, and frankly are at or below what Best Buy is doing. They are unlikely to have service-menu access unless they pursue information significantly on their own, are unlikely to be equipped any better than BBY guys are, and frankly may charge significantly more. A mom-and-pop integrator is probably on par with what BB gives you in terms of a basic ISF calibration.
And to be honest, bringing calibration to the masses is still a good thing. We love to advocate test discs for the novice who is short on cash, that won't match what a basic grayscale adjustment by a BB guy will do, yet we don't trash that.
Further, we all have to realize the back-end benefits of a massive company like BB pushing calibration services. When BB goes to their major manufacturers and tells them that their gamma sucks, or they have no access to greyscale controls, or their service menu is a nightmare, those manufacturers will act fast to listen. That benefits the dedicated calibrators too, who have long fought for decent menus and controls, and I think we'll continue to see greater and greater access to all the controls we need to really whip a TV into shape, and less and less spurious "features" that lead to an inaccurate image.
So in the bigger picture, I think you have to realize that the 900lb gorilla in the TV business is telling not only their customers, but their manufacturers that accuracy matters. That they can sell both more TVs and more calibration services on accurate televisions. That is a big big change, and in a larger sense benefits the pursuit of better images. In other words, no a BB calibration is unlikely to get the absolute best out of a display (on the other hand that's probably true of most ISF jobs with the exception of many of the folks around here who basically only do calibrations and are the pinnacle of it), but it pushes the entire range of images towards better, and IMO in not a small way.