Someone I know bought a bike years ago and on his first proper ride on it he called in at my house. He said it steers like a dog. A quick squint down the length of the bike told me the wheels were bang out. Yet the swingarm marks lined up to perfection. We got the long straight edge (rect hollow section) on it and set the rear wheel by this method, ignoring the markers. When we'd done we checked the markers. They were bang out. I mean 15/20mm out, that order of magnitude. He took it for a spin and came back grinning. Perfect transformation. I've ridden that bike a couple of times myself and it steers and handles well. Just ignore the markers! Obviously the bike has had a knock at some point in a past life. We checked fork stanchions. Perfectly straight. The yokes perfect. Probably these components were not original. Probably the headstock out of line.
We contemplated the implications of riding the bike. The main issue will be the sprocket alignment not being parallel. Next, the centre of gravity won't be quite where the manufacturer wanted it, but this will be very slight. Whatever, the bike rides perfectly well, so long as you set up with straight edge.
Even on brand new factory bikes it makes logical sense not to place 100% trust in the markers. There are simply too many other tolerances and a very convoluted path involved. A small error at the headstock, maybe within manufacturing tolerances, is bound to have an effect on wheel alignment.
When you think about it, a bike will self correct and ride straight even with bad rear wheel alignment. It'll just ride with the wheels parallel but offset. You really notice this when steering on corner turn in. The bike feels inaccurate. It really screws up the steering. You'll also notice the yokes and bars not in proper alignment as you're traveling straight, again slight though.
I recommend obtaining a decent straight edge (you only need one if you're by yourself) it's amazing what it shows up!