WAR is a counting stat, like home runs, not a rate stat, like batting average. It's not surprise (as noted up thread) that Phil Neikro has a higher WAR than Pedro Martinez, he pitched many many many more innings than Pedro did. It's likewise no surprise that Harold Baines had more hits than Joe DiMaggio. His career was 33% longer. That doesn't mean that Harold Baines was a better baseball player than DiMaggio, and Neikro's WAR doesn't mean that he was a better baseball player than Pedro. He wasn't, and WAR doesn't claim that he was.
Mattingly was a very good defensive first baseman, and has the advanced stats to prove it. Look up his Rfield on baseball-reference. He, like pretty much every first baseman, has a negative dWAR because he's a first baseman, and you get a penalty just for that. The idea is that it's easier to find someone who can play first base than it is to find someone who can play any other position (besides DH). Imagine that Brooks Robinson had played 1B; he would have been out-of-this-world good, defensively. Even better than he was at 3B. If there was no positional adjustment you wouldn't be able to account for the fact that Brooks was a better defensive player than anyone who ever actually played first base.
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