Either one voids your warranty.. or at least presents a few hoops to jump through if any warranty work needs done. To take advantage of a mani upgrade you need a tune that raises the rev limiter, since they can make use of the extra air at those rpms. Since the stock GT motor isn't built for those higher revs, good luck explaining a busted engine to a Ford. To me, the extra ~20hp isn't worth all that.
I plan on going big or not at all, so I'm saving up and making that decision later.