I haven't seen how our local shops do it but I imagine that the shaft is put in a lathe and the weld at the yoke is cut off, then the shaft is cut down and squared up, and then put back together... that way it stays straight. They can do aluminum shafts, is the one you got the same size tube all the way or does it neck down at one end? I've seen some that are really big and then neck down much smaller, usually on the trans end.
And... assuming you have a shop that can shorten it... is that shaft you picked up even worth messing with since it's also damaged?