Seems odd to me...... it seems im not aligning the bike so much as force aligning it. Im asentually dog tailing my bike. To me if it was true the rear wouldn't need changed to meet the front and if it does your front is off.yes. it doesn't matter if the marks are off there not accurate anyway. just a guide.
it can take several attempts to get the wheels perfectly in line while at the same time having the chain at the right tension.
once I have it set and the chain correctly set. I mark the swingarm and the adjusting bracket with a punch mark. then if I have to alter the chain adjustment or remove the rear wheel sometime later it can go back exactly as it was.
if I have to make big changes I redo the alignment and make new punch marks.
Now you saying there is tolerance and change the back to be inlime with the front... i get that and if what ive done is in the line of said tolerance ok. It just seems odd that they would make a bike this way.