Hmmm, the tubes heat up and the geo changes, but then they cool down and go almost exactly back to where they were before, so I dont really know what you're worried about. Bearing in mind that you can run a ring of weld around a 1" tube in one go with an arc welder, and still be able to pick it up about 4 inches back from the weld when you're done, it doesnt get *that* hot anyway.
Large bits of box section make good jigs, wood works in large enough sections but will always be changing its dimensions depending on air humidity.
Have a look on curtis' website, there's a few good shots of their jig, there are also some decent pics on goatbike's site.