Honestly, I don't think it matters that much.
newmarket is spot-on, each wafter is different.
As long as the hook is at least partially on the deck it's fine for me. I'd probably prefer the eye to be lifted slightly but wont start messing around if it's sitting flat. The critical bit for me is that that hookbait is lighter than the freebies, which it will be assuming the wafter is a half decent one.....
At the end of the day we've all caught loads of carp on bottom baits straight out of the bag so I prefer to concentrate more on where I'm putting the bait rather than worry about a couple of millimeters here or there off the deck.