With a factory Dana 35 or Dana 44, there should be no left/right offset between the transfer case output shaft and the axle's pinion shaft. With either of those two axles, the only reason there'd be an offset is if you had installed a suspension lift without re-centering the axles with an adjustable length trackbar or trackbar relocation bracket.
There's an offset with the Ford 8.8 axle which is often installed in the rear but there shouldn't be for the factory axles. At least not one that I've ever been able to notice.