First of all there's nothing special or different about aligning wheels on Nexus vs. any other hub.
You don't align by tension difference, you align by centering the rim between the axle ends, and the tension difference, if any, is a function of the asymmetry of the flange positions with respect to the centerline.
FWIW, the right and left tensions are proportional to the left and right (reversed intentionally) CTF distances. worrying about the tension difference is putting the cart before the horse. Dish the wheel properly to center (of the frame) and let the tensions fall where they may.
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