Some head units have sound "enhancement" features which, supposedly, will help improve the sound quality of compressed audio files (such as MP3s). Of course, the original encoding scheme of the MP3 needs to be taken into consideration; a 128kbps file against a V0 one will sound like crap to begin with.
For example, my Pioneer P600 has a "Sound Retriever" function, which IIRC works on CDs and MP3s. Seems to make the sound a little bit cleaner and louder, and I keep it at level 1 out of 2.
But when you say the MP3 is just being redirected, what do you mean by that? Just like a CD, a MP3 is digital audio which has to be converted to analog. There's no concern with the quality of a CD, but as I mentioned above, MP3s can vary widely in how they were encoded, which may lead to poor fidelity.
