Just commenting on an isolated aspect, as the finer points are still over my head...:
Ron, in talking about what a boxer would do, describes something that is very commonplace or should be very commonplace -- meaning we've seen this or have experienced this quite a lot: "Now, do that same atemi to a boxer, as opposed to an aikidoka, and you are correct...you are likely to get a different response due to 'reified ideal phases', and the fact that boxers get hit all the time...and just hit back.
If the boxer (uke) can hit back, he can also just "hit". So there's IMHO nothing won by leaving out the atemi. On the contrary -- by launching an atemi at uke I (1) reduce the propability that he'll hit me and (2) move his attention (partially) away from what I *really* want to do - breaking his balance. And once his balance is broken, he'll have problems hitting (back or not) anyway.
So the atemi covers up an opening during a (very short) critical phase of the technique in a way that keeps the initiative with sh'te (nage).