Some of Trek's frames may be built at the Giant factory in Taiwan, but that's certainly not to say that there are no differences. In fact, Giant has made frames for such notable names as Schwinn, and also for other box-store and private label bikes. The frames for Trek, just as for any other customer of Giant, will be built to Trek's specifications, with the wall thicknesses and tapering and jointing that they specify. I don't know where the frames are painted and finished, but there may also be differences there.

Trek is also an American-owned company with American design and manufacturing facilities. Most of their bikes are produced overseas, but they also have American production capability. My daughter's '97 Trek 850 was built in the United States, for example (if the screen-printing on the seat tube can be believed).

Giant absolutely does offer a value proposition that is hard to beat in terms of components received for the price paid, but I wouldn't go so far as to say that a Trek is basically a Giant with a different logo, and that there's no good reason to pay more. Different people will place a different value on the factors noted above.