Howard has more 23 more home runs, 5 more doubles, and 4 more triples with runners on base in 50 less AB's than with nobody on. Dunn on the other hand has 43 less home runs, 56 less doubles, and 4 less triples in 500 less AB's than with nobody on. His AB/HR, AB/2b, and AB/3b ratios and BA all get worse with runners on, risp, risp 2 outs. While Howard's AB/HR, AB/3b, AB/2b ratios and BA are all better than or equal to what he does with nobody on base.
WAR does not account for the fact that Howard produces more with his hits than Adam Dunn does, because he produces more with runners on base and Dunn produces less with runners on base.