For example, one is hand-welded in Germany, while the other is machine-welded in Taiwan.
Regardless of the keeping locals employed and keeping the money where it should stay arguments, I'd trust a hand-welded frame from southern Germany than a machine processed frame.
In addition, if the frames are made in house, then a certain amount of new technology can be implemented directly into the manufacturing process with minimal lead and testing/refinement periods.
One example is making frames to test these in house:
PINION / P1.18 / DRIVE TECHNOLOGY
The turn around time is much longer if the welding is done by a machine halfway around the planet.
It also reduces the cost and shortens the development cycles.
For a precise example, why doesn't the Surly CC have the handlebar rotation stop welded to the frame? It just seems like an oversight to me because the extra material would literally cost 2 USD at most.