I have no experience with expensive titanium frames, but on every bike I've seen, rear wheel installation required eyeballing the distance of the wheel between the chain stays and, to a lesser degree, between the seat stays before tightening the axle fasteners.

Does this frame have adjustment screws in the dropouts that may have been damaged or disturbed? A millimeter off in the dropouts translates into several millimeters at the stays.

The OP says that he flipped the wheel in the frame and thinks that the problem appeared in reverse, but he doesn't sound certain - the difference was that small (2mm closer to one stay is only 1mm off center). If I flipped any of my wheels, I'd assume that I would still need to visually inspect and manually correct the distances to the stays. If I ended up 1mm off center (as the OP experienced), I'd simply re-adjust - I wouldn't agonize about either the wheel or the frame.