Excellent post Ledyard Sensei! Your explanation is dead on.
My experience is that the people who are able to throw me with either magical ease or no touch at all are the ones that would best be able to have destroyed me with an atemi.
After following your suggestion to train without possibility of atemi I would suggest trying to opposite. Let uke know that you intend to strike them with as much power as you can muster before throwing them. You will be amazed at how easy these throws will become without need to actually strike.
This of course will only work if uke behaves like he believes you, and has the requisite ukemi skills to prevent you from hurting him.