I'm not sure aikido atemi at their best mirror what karateka do. The use of the hips seems very different to me. Which is not to say that learning to strike as they do is not beneficial. I just don't think it is the best way to deliver atemi in an aikido technique. Whole body delivery of power through knee movement and body movement as opposed to using the hip snap. Gozo Shioda talks about transfering the energy from the ground using the knees in his autobiography, not using the snapping of the hip forward and back as is often taught in karate. But then, I was never very far along in karate. And I still need to work on this, as my understanding is still incomplete.
I do notice that many of the atemi in yoshinkan basic kata seem designed to hit, not just distract, and they generally do not interupt the flow of the technique, as demonstrated by the top instructors. The atemi often seem to be as the foot plants and the body turns (as in yokomenuchi shihonage), or in a body change (as in shomenuchi iriminage ichi), so that the atemi is flowing out of the movement of the whole body. In my experience, etc. etc.