The point is shouldn't the guy with the higher WAR be the MVP since WAR is the holy grail of how good a player is??
I'm pretty sure the issue there is with the voters, not with WAR. James's article was actually about looking at MVP voting over time, to see if voting had gotten better now that advanced metrics are available. He concluded that it had, but there are still misses (and in this case, giving the award to the guy who won the triple crown probably isn't really a miss, even if Trout was better).