Of course I could be wrong and "Girls" could end up featuring anywhere, but Mandy Moore is obviously being used here as an "actress" rather than a "singer", and having someone else perform the end credit song would mark the difference out in the lyrics of "Girls" that the song is
about Rapunzel rather than being sung
by her.
Going by that explanation, having the different voice would make it clear it wasn't Rapunzel singing and, in all likelihood, give the song more of a chance of being a hit for Disney, to whom Miley is signed, of course.
Having different voices sing the songs at the end of a movie isn't anything new...the cast of Enchanted didn't sing Happy Ever After, after all, and that was a quasi-pop/still part of the musical kind of song. Then again we have had deleted songs (Hunchback's Someday, or Pocahontas' If I Never Knew You) re-inserted back into the films by way of pop treatments on those tracks, which begs the bigger question: if the choice was to use a radio friendly, audience attracting song by Miley Cyrus for the end credits, why didn't they get Menken to pen one, or use something that might have been written and then unused in the film, like Hercules, which used a different song to Go The Distance on its international release.
My guess is that "Girls Just Want To Have Fun" is going to be the underlying marketing tag for what will be sold as an animated romcom. We will hear it on all the TV spots, a final trailer, on the radio, as a single, etc, and eventually in the end of the film itself as the credits pop song. Although I'd have preferred a Menken original, again I can see how they're trying to position this, and not only does the song say what they need the marketing to suggest, but it's an instantly recognisable track, which will do two additional things: appeal to the women (now probably mothers) who danced to Cindi Lauper in the 1980s, thus dragging their families to the movie, and appeal to Disney's Miley followers, who will buy the single, download the video (with animated clips in it, natch) and go see the movie too (hopefully, as Disney is hoping with the name change, dragging their bfs too).
So, when you think about it, that all kind of makes sense. Now you just watch that list of songs be declared phony, and my extensive reasoning go to pot!