It is best not to pay much attention to those marks. Assuming they are stamped accurately in the first place, they will still be a bit off after the axle nut is tightened down. As you discovered.
You can use a string wrapped around the rear tire and pulled forward on both sides to the front tire. If you line up the string with the edges of the tires just right, it is possible to make great fine tuning ajustments to the rear axle.
Or you can sight down the top of the chain from behind the bike. Have to lean down quite a ways, but it is possible to see if the chain links are straight or not. And you can spin the tire and to if it remains straight all the way around.
I was not making fun of you personally; I was heaping scorn on an inexcusably silly idea -- a practice I will always follow.