Yep, I noticed (on my '95 ZX-6R) that they are not entirely accurate. I don't know about the '05 636 ('cause I haven't adjusted the chain yet, despite having done over 20,000 miles on it... [:I]), but I assume it will be similarly inaccurate.
Most bikes have this problem. Sometimes it's really obvious, sometimes it's not so obvious.
Edite: From memory, the marks on my '95 ZX-6R were off by about 1/4 of the distance between lines. Not a lot, but enough to upset the handling if I used them exclusively.
Those marks are almost always off. To align a bike I use tiedowns from the ceiling to the bike to make it stand up straight without a stand. Then I rubberband 8 ft fluorescent light bulbs, that I fished out a dumpster, to each side of the tires. This makes sort of a tire sandwich. With these two bulbs as straight edges you can really see how the wheels are not aligned.
You must make sure that the front wheels is straight, then it is easy to see how the rear wheel must be moved in order to align it with the front wheel.
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