You mean throwing off the 4-bolt alignment.
No, it's the side to side alignment of drive to the internal spacers, wheel mating surfaces, etc all the way across to the frame and axle nut.
The reason you loosen the four nuts that mount the drive to the swingarm, and tighten them after the axle bolt is torqued, is to allow the final drive to self-adjust and keep the drive and driven splines aligned when you torque the axle.
The only thing the four nuts have to do with alignment is to screw it up if they are already tight and the final drive can't self-align.
Not trying to sound preachy, just feel like the clarification is important.