I had previous suggested the idea of 'audio interface profiles' that could be configured and recalled because I was also worried about track (in ST4 now Bus) routing changing depending on what I was connected to. It was also going to make things a little clearer for me when prepping my iPad at home and not having my mixer to plug into to expose the interface to ST - in effect, it could still show me my mixer's interface inputs.
So far I haven't run into any issues with the way ST3/ST4 is working with regards to the way it just automatically remembers and recalls interface routing. That said, there are still times when I'm working on some song config in ST at home, without my mixer, and wished I could setup some specific track/bus routing, and can't. I have to remember to do it the next time I'm connected to my mixer. Small inconvenience at best, but still...