I can't exactly speak for karim, but that was the effect seen in pyPianobar when pianobar is not in the current $PATH.

I think the only logical fix for the binary is to leave it where the autobuilder put it and link it in /usr/bin (this is what I have done on my N900)

As for the config, the logical place to me would be "~/.pianobar/config". This is where it seems like 90% of apps keep their configs anyhow, and putting a config for a per-user app in non-user space is so 1990's