Can you give me an example of these "advanced" sketches? Because as far as i know, all the arduino software does is wrap your code around what i pretty much wrote here and then sends it to avr-gcc. I'd like to know what else it does. I know of a few hardcoded defines, like the arduino version (which is troublesome even in the arduino program as i've heard), but i can't think of any other.
Also a note, when you use eclipse, you're still using avr-gcc, which is exactly what avr studio 5 uses too. So there shouldnt be any differences there other then possibly the gcc version.