From memory the input shaft splines are different too. I know I tried to put my automatic transfer case onto my manual gearbox, and it wouldn't fit.
The AT transmission is longer than the manual so the output flange is closer to the rear axle. Using a fixed flange output means the U-joints end up a bit farther apart, which improves the U-joint angles.
I imagine they used a slip-yoke driveshaft on the manual because slip-joint driveshafts are expensive, with all those extra flanges and splines and whatnot.