I looked in my french technical manual, and it shows the tensioner being put back before the cover, and I can't see how tightening the cover could effect the tension of the chain. Maybe I haven't understood what you mean though.
As I see it, once you put the head back on, with the chain correctly positioned on the sprockets, your cover should be just that, a cover.
Take care, I don't know if this will help you much.
PS: Have you pushed your chain tensioner rod in before instalation