Can't speak for Naruto Fandom, but I see this exact thing in Harry Potter. Many times Harry is exactly like that. I even read a story with Draco/Girl Harry, which was posted in Harry/Draco section. Girl Harry did peak my interest, I imagined that he would be turned into a girl and back. But no, it was Girl Harry in all chapters and the only things that connected with Cannon were:
The name;
Black hair;
Green eyes;
I suppose that it's a different sort of Mary Sue.
People do associate with their favorite characters and write fantasies about it. It's a part of overall fandom fun.