Wow, I'm getting confused...
It seems like there's two lines of communication going on here, one that refer's to the _sound_ of a piece, and the other that refers to the way it's written on paper. Personally, I still write directly to score -- Finale, step input, note-by-note -- so I'm always thinking in terms of how an idea is presented on paper (and yes, this does immediately take into account concert pitch, transposing instruments, and so on). So I can't quite understand where the confusion's coming from in this thread... But it's bringing up some interesting thoughts, in my head anyway, about what we mean when we say "score".
In fact, I'm going to start a new thread in "Orchestration...", just to see where this discussion goes!
J.