I'd argue that he's better because he has mastered more than just one format. If we have a tie in one category, and one of the players has a strong advantage in another category; then they'll come out as "better".
Imagine two people of equal ability at ice hockey. You wouldn't say that one is better than the other at ice hockey because he's better than the other at field hockey.
Adding my edit to a below comment here:
Probably the best analogy here is association football -- the normal, standard game can end in a draw. During the World Cup and other elimination tournaments, a completely new rule, not part of the normal game, is introduced allowing games to be decided by penalty kicks. Is the fact that Italy beat France in the 2006 World Cup final on penalty kicks evidence that Italy's team was "better at association football" than France's? Many people would argue that it's not.
Rapid and blitz (and armageddon) were part of the meta-rules of this match, but then your argument only works if you say Magnus is better at the meta-sport called "winning the 2018 World Chess Championship" -- which I'd agree with, but it isn't the same thing as being better at chess.
Probably the best analogy here is association football -- the normal, standard game can end in a draw. During the World Cup and other elimination tournaments, a completely new rule, not part of the normal game, is introduced allowing games to be decided by penalty kicks. Is the fact that Italy beat France in the 2006 World Cup final on penalty kicks evidence that Italy's team was "better at association football" than France's? Many people would argue that it's not.
I've competed at a high level in a hobby of mine, and it was well known that the winner of a competition was never "the person who is best", it was "the person who is best in the competition environment that day". No matter what rules you have, that will always be true. And that's okay.
I wouldn't be surprised if Carlsen would soon again have a comfortable lead on the ELO ladder. He was once at 2882.
I am however happy that he had such a worthy opponent in this tournament!