Fangraphs uses a FIP-based WAR. They have an RA-9 WAR, though, that has him at .9 WAR in 84.3 IP.
Seriously, use Fangraphs, it's better. The articles are absolutely amazing and the stats I find are much better.
Honestly, it does, to an extent. not so much as to what you outlined, but just one example, advanced stats has made me appreciate the strikeout more and pitching to contact less.
Fair enough, there's some merit to each side. And don't worry about it.
I think the nice part is that no matter how you look at it (except for Cards fans), Colby is damn good.