The power of these techniques has been radically overstated by both enthusiasts and critics.
While the science underlying these techniques is true and the techniques do work, they are not the Philosopher's Stone of game design. Classic behavioral psychology is a nice simple model of certain basic mental processes, but it falls down when trying to explain the totality of human behavior. There's a reason why modern psychology consists of more than just behaviorism!
The over-emphasis on these techniques has been seen on both sides. On the "enthusiast" side, a number of game developers have assumed that fun didn't matter; they just had to have a reward structure. This has generally proven untrue, since they are competing against other games that are both fun and have a good reward structure. Good contingencies are helpful to a game, just as good graphics or good music is helpful, but not sufficient.
On the critical side, there have been plenty of claims that reinforcement schedules are too powerful, that they compromise the will of the player. Again, reinforcement schedules are useful and effective, but don't represent the total sum of human psychology or the game experience.
Consider the use of loyalty cards at a coffee-shop. It is a contingency, exactly like the game contingencies covered in the original article. Indeed, it should be more powerful than game contingencies because it provides tangible real world benefits. And yet I don't think anyone would argue that "buy 10 lattes, get 1 free" is manipulative or too powerful for the average person to resist. (The chemical properties of caffeine notwithstanding.)
Contingencies always exist.
Nearly a century after Watson defined behaviorism, it's still misunderstood. Many people seem to assume that there are no contingencies in a game unless they're explicitly added. This is simply wrong. If you're playing a game, there's something in there that's rewarding for you.
It doesn't matter if the reward is intrinsic (self-expression) or extrinsic (an achievement). If the player doesn't find something rewarding in the game, they don't play it. Any pattern in how that reward is provided is a contingency of the sort described by behavioral psychology. They exist whether or not the designers are aware of them.
The original Behavioral Game Design article was fairly clear about this:
"Every computer game is implicitly asking its players to react in certain ways. Psychology can offer a framework and a vocabulary for understanding what we are already telling our players."
Unfortunately, many people still believe that contingencies are some sort artificial additive: MSG for video games. This just isn't true. Contingencies are fundamental to games, so much so that I'm not sure it's possible for something to qualify as a "game" without at least one contingency.
There is no Skinner Box.
Furthermore, when critics of this approach describe games as Skinner Boxes, they completely miss the point of the Skinner Box. The goal of the early behaviorists was not to create an artificial environment where some new form of mind control could happen; it was to create a simplified model of the real world.
It was an attempt to understand learning at a fundamental level by creating the simplest possible operant learning task: "Press lever, get food." Like all scientific experiments, it was an attempt to isolate a phenomenon, to remove distractions and alternative explanations that could confuse the issue being studied.
A Skinner Box is completely unnecessary to create operant conditioning. It is an experimental tool for studying conditioning, nothing more. There wouldn't be any point to "putting players in a Skinner Box"!