Some parts must be reassembled in the same way they were because that is how they were made/machined--piston rods, main bearing caps, same for the bearing caps in differentials.
Other times you will see directions to mark parts that could result in vibrations--flexplates and torque converters, drive shafts and yokes.
Think of it this way, if you are replacing the flexplate, or the torque converter, does the mark remaining on the original part have any significance to the new part?
However, if you don't mark something, and you are reassembling rather than replacing a part, and the customer keeps coming back and B*tching about some new vibration (Princess and the Pea), well, if you didn't put it back the way it came apart your chargeable time just went into the toilet.
So, goal one of marking is to get it back together correctly the first time, and without having damaged anything.