Tunesmith, I believe that the reason why Tom threw that awkward F chord in "Jimmy Newman" was because the song was meant to be written awkward, as the guy in the song was facing an awkward situation.
Of course that song is not one of those pleasant-to-the-ear kind of songs, and it shouldn't be. It's pretty much like "Crucifixion" by Phil Ochs, done in a less technical way.