Depends on what misalignment you are speaking of. There is perpendicularity, parallelism, runout, etc. All those are built into the motor, bell housing and tranny mating surfaces and bores, with some tolerance. The clearance in the mounting holes on the parts will allow splines and a pilot diameter or two to engage. (Sometimes there are guide pins).
If there are no burrs, stick ups, damage, cracks or warpage, torque to spec and you are good to go. Just be sure surfaces are mated evenly with star pattern or cross torqueing.
Edit: Just looked at Lugnutz web page. Very nicely done and very informative. Use his info if it conflicts with mine.
