I have no personal experience, but from what I have read they wont clean up the cuts...meaning no sanding of cut edges and therefor you have to be much more careful of handling as the edges will be very sharp.
Honestly, as incompetent as most of the HD\Lowes kids appear to be, I'm not real sure I would want them cutting anything that needs to have close tolerances.
It may cost a little more, but I would rather a real glass company do the cutting...it is something they deal with on daily basis, and one would hope that would mean better quality of workmanship.