I don't think you can compare just by looking at points against a common opponent. Lots of other factors. Bottom line is, which I stand by, is that most agree that the 49ers are the best team right now as far as power rankings are concerned, and given (1) who is on their roster, and (2) what they have done so far, that isn't something out of left field--it's a perfectly understandable position, and one I happen to agree with.
And I think it's silly to pick apart both games to try to justify why one win is better than the other. But if we were to do that, there are some obvious differences. The Cowboys played the Giants, a division rival, in week 1. They had time to study and prepare, and given that it is a divisional game, they had extra motivation and they had extra intel (they've played this guys recently, even if it wasn't this year). The '9ers got them on a Thursday night. Shortened rest. Shortened prep time. I wouldn't expect them to be as sharp as a week 1 Cowboys team playing a division rival. Second, again, it's a Thursday game. Thursday games are typically sloppy. You don't often see a team at its best. Third, the Giants fought instead of laying down, and with 2 weeks to learn from week 1 mistakes, they cleaned up some things from the week 1 game. This wasn't the same quality of opponent that the Cowboys played. Fourth, the Cowboys got 14 of their points from a defensive score and a blocked kick that turned into a scoop and score. I'm not knocking the defensive and special teams effort. But the scoring probability on those types of plays is low, and usually dependent on luck. Even if you get the blocked kick, the odds of the ball and players aligning just right on the field to enable the scoop and score is extremely low. And fifth, you can't just take a single common opponent game in isolation to make any sweeping judgments. Sometimes, the lesser team just has better matchups against that common opponent. Other factors as well. So, to try to answer your question, while I think it's fruitless to try to draw conclusions and make comparisons from this one common opponent, there are lots of reasons why any such comparison doesn't change my opinion. I mean, putting aside the points, you could look at game stats and try to argue that the 49ers are "clearly superior" based on this common opponent game. I can see some fans trying to argue something like: "Most of the Cowboys' actual points were just lucky. They put up less than 300 yards of total offense, which doesn't normally net a team 40 points. In comparison, the '9ers put up over 400! The Cowboys' passing game was almost nonexistent, yielding less than 150 yards and no touchdowns. The 49ers? Over 300 yards and 2 touchdowns." And on and on we could go. But ultimately, that would be just as pointless.