Speaking as a biologist, I can assure you that the protective reflexive reactions (especially protecting the face/eyes) are indeed innate and not learned. They can be tuned and honed but they are, at their most basic, innate. The reason while toddlers run into stuff is because their nervous system is still developing and all their reflexes are not yet functioning at full capacity. Most of the reflexes of a newborn are built around eating. The other ones come later.
As for your point about the "wisdom" of hard, controlled atemi at newbies, I understand what you're saying. I was offering that more as an illustration of how to provoke a response. I think that if newbies are allowed to see that atemi can be quite real that it can help them to respond more realistically themselves.
The notion of a learned response to atemi is precisely because of the clothes line example I offered. We flinch at the clothes line because we don't expect it. We don't "flinch" at atemi in kata because we do expect it and therefore have to learn to emmulate the "flinch". However, making the atemi more "real" in the beginning may help to illustrate the need for the reaction.
Did that make any more sense? (I'm not sure it did to me...