Originally Posted by
silver_ghost
..I seem to remember reading somewhere about bringing the spoke pair that straddles the seam up to higher tension that the rest of the wheel to compensate for irregularities.
Yeah, that's where you'll eventually end up - balancing the best possible spoke tensions against the best possible trueness. With a rim that isn't perfect to begin with you have to take your pick, or find a working compromise. For a disc-braked mtb for off-road use I'd give spoke tension priority over trueness.