Hmm - not sure how to answer that.
As I understand it, mp3gain stores a "marker" in the id3v2 tag, to say what the overall gain level is. When you apply changes, it then applies a general multiplier to each frame, to affect the gain. (Hope that makes sense?!)
So, to answer your question, it does both - but the key is that it (allegedly - I have my doubts) does affect the audio data

By the way, sorry for the slow responses - the notification messages are being filtered as Spam by hotmail