Also, I don't know how it would change the evaluation of FIP, but I think it is incredibly meaningful within WIS (if you are going to use FIP) the order in which outcomes are determined. IIRC, it goes: Is it a hit? Yes> Was the hit taken away by a good/great play, Was the hit a Single/Double/Triple/HR, Was Double/Triple/HR reduced to something less by a great play, etc... or something like that.
I may be thinking of this incorrectly, but the fact that the determination of "Hit" is made before "HR" makes an HR less damning to a pitcher's production... i.e. it is quite possible that a pitcher that gives up a lot of HR can "always" have so few runners on base that an ERA/WHIP like Sheldon's with a high HR rate makes sense, and is not just luck.