I think this may be a time where atemi is a smaller part of the equation; I don't make any claims at expertise, so please feel free to tell me if this observation is off base Mr. Ledyard.
This is only an opinion, and is open to adjustment.
Especially because the solidy grounded attacker won't jsut flow with you, the technique required will be an omote version (entering directly) and yes you are right that the Aikido person will have a hard time landing an atemi on the trained striker. It is the action of the atemi that causes the striker to defend. If he is defending he is not hitting at that instant. That is when movement is possible without the attacker tracking you. The action of the atemi causes the attacker to "give' you a technique rather than you tryiong to take it.