He's not evil in "Non Sequitur" -- just a loser.... By your reasoning, Star Trek II: The Wrath of Khan is a Spock movie, and Star Trek: Nemesis is all about Data. That's just silly. Harry's the one in every scene of "Non Sequitur," not Tom. And Harry's the one with the goal -- getting back to his reality -- that he sets out with during the first scene and achieves in the last.
Basically correct about alternate Tom's loserdom.
The above at least makes a clear and sensible argument. But the beautiful theory is killed by an ugly fact, which is that Harry's way back is basically handed to him by the observer, Cosimo. The point is not that Harry has to solve the problem of reaching his goal. Indeed, the point is not even Harry deciding to go back, which is why his decision is so briefly sketched. He really was aimed at going back from almost the first scene. This would be implausible were it not setting up the real plot.
The big scenes that were obviously intended to have the emotional intensity or payoff were Harry's appeal to Tom, then Tom's rescue of Harry and Tom's self sacrifice. It was Cosimo and Tom who got Harry back, so the episode surely wasn't about Harry achieving his goal. Only if you assume that the episode was about Harry and the peculiarities in the dramatic structure were merely incompetence can you really argue that Non Sequitur was a Harry Kim story. Otherwise you're begging the question of what the story is about.
Whether or not a character wins isn't really very dramatic, not like making a choice. Or a favorite substitute, making a self discovery. Which is why Wrath of Khan is indeed about Kirk, even if Spock is arbitrarily sacrificed to the script gods so that Kirk can "feel young again." (You didn't really think that a starship would need to have a steam pipe reconnected by hand, did you?) I have no idea what it means to say Data sacrificed himself, since there was no plausible reason to think he couldn't make up a backup disk. As to what Picard, I have no idea, but that seems to me to be pretty good reason to regard that script as a failure.