For only the second time in nearly a decade I'm going to disagree with you here. You're one of the most logical posters on the board and you don't usually miss the intangibles, but I think there's a serious intangible difference between Shogun and Joanna.
You mention the difference but outside the context of the Shogun fight - sustained beatings. Shogun had taken a sustained beating since the bell rung to start the fight. Round after round a superior fighter beat on him like it was a sparring session with a rubber dummy. So, when he FINALLY tapped (and he did catch SOME flack for it) he was simply accepting what he, Jon, the crowd, the refs, the judges, Dana and the fans already knew. He had run headlong into a superior athlete/fighter.
Joanna on the other hand got dropped and hit a few times in the first.
One of them had taken a sustained mauling and the other lost her equilibrium and didn't like getting hit.
Now, don't get me wrong, I know the way I'm choosing to word this paints Joanna negatively, but I don't see it that way. I just see the difference. I'm cool with both cases, personally. There IS a difference, IMO, though.