I don't know exactly how WARP is calculated, but I was under the impression that it did use FRAA.
Just for arugments sake, EQA (adjusted for this season):
Pujols: .350
Howard: .340
FRAA (adjusted for this season):
Pujols: 17
Howard: -15
FRAR (adjusted for this season):
Pujols: 25
Howard: -5
Yeah, Pujols blows Howard away in every category...

