If I remember sometime back a few years, one of the heavy users on this site said the cam lobe is round on the back side. I think it was during the time when the modified cams were being created. Perhaps it was SISF, T-Cro, or maybe someone else. Please don't misconstrue that I am saying they did say it because I'm not going to dig for it on the forum. I would tend to agree with this, but have not ever put a set of calipers to it. At this point SISF should actually know if this would be correct due to the fact that he has re-designed the stock cams for his "Torque" grind. Maybe he's listening and will put it to rest. I can't find the mention in the shop manual anywhere where you refer to "the somewhat horizontal (but slightly higher) position on the cam lobe as the position" to use when checking the valve clearance.
I did find this in the shop manual, and it would be the specific method to use. Notice it says it "may" result in improper adjustment. My opinion is that many don't know where the cam needs to be when checking the valves, so following the manual exactly is the best way for these individuals. If I'm wrong about the back side of the lobe not being "round", I would gladly retract my recommendation. I would probably do the valves the same way though on my own bike. Are you going to tell me you pull the plate off each time and line it up by the marks?