Which manual is that? I'm not at home to check, but I am pretty sure that both Haynes and the factory manual say to drain the sump (LH side of crankcase) and the oil tank (on front frame tube), but say nothing about the cam cover. The camchain comes up from the crankcase in a big wide hole, so there's no possibility of a vacuum in there.
As long as you have drained from two places (three if you count the filter housing) you should be fine. And cam covers do seem to get stuck on very tight. That's probably a good thing in terms of oil leaks etc.
(Sorry, read your post again. You mean the manual you got from this site? What page? I think there might be a misunderstanding here.)
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