See, I don't think that is necessarily true either. Not trying to be argumentative, I swear.
It's possible to have new champs who have yet to face dangerous contenders, like Woodley and Wonderboy. Or you could have a situation like LHW where DC is the champ, but Jones is the best LHW. Even had Lawler won, I think it would be reasonable to claim that Condit was a better fighter than he was, etc. Or you could have a situation like LW where a guy like Khabib seems unbeatable to some extent, but has been kept out of action because of injuries.
I think that as the quality of MMA fighters continues to rise, we'll see more and more parity toward the top, so this type of situation may become more common.
I think this discussion mainly pertains to newish champs. But even champs who haven't cleaned out their divisions, like Joanna, can be considered the best because they have shown they ought to be favored in pretty much every match up, even though it is quite plausible that they could lose to a fighter in their division.