Mine measures 560 mm on both sides (at 1.25 increments back from the loosest mark). Your 500 mm number is off, but it is the 5 mm discrepancy that is pertinent here. There are five different ways to check the alignment, and, in theory, all five should agree:
i) chain-adjustment marks on swing arms agree
ii) axle center to swing-arm pivot distances agree
iii) front and rear sprockets are in the same plane
iv) front and rear tires aligned (when front wheel is straight)
v) bike tracks straight while you ride on a flat road when bike is vertical and you let go of the handle bars
On my last bike, the swing-arm marks were unreliable because the pointer clip could rock (rotate about axle when the axle nut was loosened) to move the pointer +/- half an increment. When I adjusted the chain on the Z650, I thought the pointer clip was less sloppy, but I did not actively try to rock it. If your nut is still loose, see if the pointer can be moved by rocking the plastic piece CW or CCW.
To check the tire alignment on my last bike, I used a ProAligner. It's just a specialized ruler for eyeballing (with one eye) the tires and comparing measurements between the right and left sides. (The ProAligner company may have gone out of business, since their website gives an error. This tool was referenced in an article in Cycle World magazine -- March 2011, p. 77.) To double check the tire alignment, I messed around with a laser -- the beam skimming the edge of the rear tire and pointing forward, then referenced to the front tire -- and I was satisfied.
Once the alignment is verified (by whatever method), always turn the chain adjustment nuts by exactly the same angle on each side (e.g., tighten by a 90-degree turn of the nut on each side), and your alignment should stay spot-on over the life of the chain.
Good luck and keep us informed about what you learn.
