Kirk-
I could see it going both ways. For now, just having two separate images would be fine, but the functionality to do scripting of some sort could open up new doors for how we as users approach our work flow.
Heck, if I could integrate a Photoshop action into the upload process, I would be in post-processing heaven.
Since it is a somewhat more advanced feature, maybe making it an option to enable a script in the various output panes would work the best, and have scripts editable in some centralized fashion. That way you could just click a box that says "use script" and select which one from a drop-down (in the option pane).
I hope that made sense.
-Joel
P.s. I just discovered code replacement today. Pure genius.