Couldn't you just cut out the floor of the gear basket at the back edge of the sunroof? Then you'd have the same look from the sides but the sunroof would open.
BTW, I *think* part of the reason most of the Xterras you see have the gear basket still on is because more XE's are sold than SE's, so many people have nothing to gain from removing it. If I didn't have the sunroof I would never take it out, it's a great place for wet tow straps and the like.
(Anybody know if I'm right re: sales of XE vs. SE? Around here it certainly seems like their are more XE's...)