I think the top and bottom lines are different increments, it appears that the hatch marks are too thick for fine adjustments so they put lines at the top and bottom at different adjustment points for finer alignment.I'm just wondering if anybody noticed the chain adjuster on the swingarm on the 08 busa it is not in the center of the swingarm and when you go to adjust the chain it moves the adjuster with the lines on it on and angle to where the top and bottom lines have a tough time lining up correctly. I have noticed this on the 08 busa's and also on my friend's 05 gixer 1000, most every other bike I seen including my 99 busa and my 04 cbr 1000 are all in the middle making it alot easier to adjust not that it's a big deal but I find it odd and that know one on the forum has ever brought this up,just my 2$...
But, I don't use them, I use the "hole guage" end of a dial caliper. I adjust the chain up till it moves about .5 to .75" up and the same down, then I verify both sides of the axle are the same with the end of the dial caliper, (from the end of the swingarm to the back of the axle carriers) THEN I tighten my axle nut (before tightening/locking the adjusting nuts) after tightening the axle nut, I reverify the chain slop, if it's ok then I tighten the adjusting lock nuts, if not I readjust the chain, but what I have found works best is to lock my axle down before I tighten the adjustment bolt lock nuts.