Wow. I have rarely seen such a well written and thought out post on such a complicated topic. I'm going to read it again to see what else I can glean from it.
Myself, I would not focus too strongly on 'atemi as distraction.' If I give an atemi, I may not actually strike my partner if they do not block, but I pretty much always get a reaction as if THEY believe I *might* strike them. 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.
Which is why outside of that 'reified ideal phase' you must at least strongly consider almost always actually making contact, and not hoping for a distraction. And that contact must be mechanically sound...otherwise your wrist breaks, and/or they smile and hit you back
I think the best counter to 'reified ideal phases' is cross training. Working with different arts, working with people from different arts in your art, etc. And even when dealing with karateka who are also trained in aikido, you must be aware that they know you are going for a throw...and that there may be a certain degree of 'tanking' for their own safety (or maybe yours).
I'm not sure how this awareness affects my previous post...but it is an important one, and one I probably do not physically practice under enough.
As to the atemi in some of the typical kaiten nage examples...yes, I would modify the severity of the strike so as not to preclude my end objective...which may change precipitously depending on the responses of a particular attacker. Sometimes the atemi is the throw, sometimes the throw is the atemi, sometimes the technique is the atemi...and on and on and on...