While that's ultimately not my own take on it, it's still a perfectly plausible, thought-provoking theory. In all honesty, I can't rule it out, either. The beauty of this show, particularly with that final episode, is that it lends itself to quite a few different interpretations; and some of those can easily overlap.

This theory makes perfect sense to me. It even conflicts minimally with the creator's and writers' intention to make the show a philosophical exploration first and an empirical mystery second. Even the seemingly tangential trials such as Emily Noonan seem to be a sign that this training and conditioning was working he was seeking out conflict and upsetting the established order even when unharassed by Them.
Scott Jordan is another good example. Think of that in the terms of trying to condition someone through interpersonal skills alone into your line of thinking. It worked, enough for Jordan to become an asset for exactly as long as he needed him. Then, he ends up incidentally discarding Jordan in a fashion that completely incapacitates everything him from putting what he knows to use in a fashion that won't make any headlines other than the Weekly World News. In the course of investigating Them, he even uproots probably the only man on Capitol Hill that would both believe in this Organization and do anything to stop them, in addition to one of the few lawmen who would fit the same parameters and be able to aid in such efforts!
Hell, New Phoenix? Do I even need to elaborate!? You could make a sound argument that these subversions were his mission all along, but that'd be too much conjecture, while what you've put down is truly worthwhile.
Thanks much! Not only is this a fantastic theory that connects all the dots, it ties together
so
well that it actually transforms the show's final moments from a season one cliffhanging into a proper ending.
Wow, this topic made my day. Time to rewatch!