My approach to gain staging is primarily to keep my entire mix from clipping at the output. And, like your example states, the remedy for clipping can easily be compensated for as far as rendering an AIF. Mathematically there is plenty of headroom internally to add and ultimately subtract.
In the example where creative/deliberate distortion is the goal, is it typically the same kind of math though? Take something basic like the Gain knob on Guitar Amp Pro: Is there a neutral setting for it? (There doesn't seem to be) The numbers that distinguish the settings are arbitary yet it does both +/- gain...
Anyway, is it redundant to use the Gain plug-in to reduce the signal before hitting the G.A.P gain stage where the signal will be cranked and even cranked some more on the Master knob (and alas, taking the overall level down via the output slider on the bottom if ye so desires...)?
Computer: 2 GHz Core i7 MacBook Pro w/ 8 GB RAM
OS X 10.6.7
Audio I/O: Apogee Duet
Controller: Novation 25SL MkII
Monitors: Mackie HR824