when one could just switch over to AVRStudio/WinAVR/AVRDude
Assuming that that's possible. No AVRStudio on linux or Mac, for instance. One of the things that Arduino does rather nicely is make the "experience" very similar no matter what platform you happen to have. While I agree that twisting yourself out of shape to do something in Arduino-land that is difficult there (say, supporting a different CPU, and incorporating third-party binary or assembler libraries), I also can't see the opposite - saying "oh; I need to program in real C; I'll have to abandon Arduino!"
On the third hand, it you DO twist yourself into making arduino do something new, you have a somewhat larger audience for your results...