i don't normally throw the atemi at the end of the technique, but i usually am in a position to deliver the atemi, be it fist, knee, choke, kick, dropping kitchen sink, at moment notice, i.e. i am not unbalanced or distracted. same goes for when i take ukemi. just because i am on the floor doesn't mean i am helpless and allow you to deliver the atemi unimpeded.
I think your last point is well made phi. actually your whole post is well put. if I for instance attempted to strike my instructor when he was a grounded uke i'd end up exactly where he was except maybe not in as good a shape. we are constantly reminded that when uke goes to ground it is just the beginning.
We are also taught that it is the job of uke to remain extended through which ever limb is being held in the pin and also through any contact with the floor. this allows him/her to 'feel' any atemi or other change in either nage's intent or the technique as soon as nage begins to apply said change. an alert uke can become nage in a split second even from a grounded position, as I find out every single class
I would agree with others who have said that if atemi is to be applied it is better to do so before the pin or throw. from my- relatively inexperienced- viewpoint delivering a strike to a grounded uke changes the balance between both uke and nage and a whole new situation may arise. one that nage may be unprepared for. well in my case anyway.
Of course all of the above is only relevant if uke has gone to ground on their terms. otherwise the strike could be redundant as it would have been already applied. by the pavement.