I was looking through my old thread for when I fitted a Boyer Bransden ignition:
http://www.xs650.com/threads/boyer-bransden-ignition-1981-yamaha-xs650-sh.48040/#post-484422
In Entry 1 there is a photo of my cam with a drill bit in it to show the chain was set correctly. This photo was taken after several hundred miles on a new cam chain which looked slightly out at assembly like yours.
http://www.xs650.com/threads/boyer-bransden-ignition-1981-yamaha-xs650-sh.48040/#post-484422
In Entry 1 there is a photo of my cam with a drill bit in it to show the chain was set correctly. This photo was taken after several hundred miles on a new cam chain which looked slightly out at assembly like yours.