I think I said it all in the first place: "I talked with my Sensei aobut this, he said it probably has to do with te lack of any control over the fall in such throws, compared to the typical Aikido Ukemi in which one elects to fall to "save himself".
Note the last statement. Most other throws we have, including, Shiho-Nage, Kote-Gaishi, Ikkyo.And Kaiten-Nage, and many others, in all of those Uke controls his fall, and makes a choice to save the broken joint this way.
Even if I loose my balance, I still have a choice and control in those falls and many others. I do not have that choice nor the same control in Koshi Nage or the shoulder throws (forgot the Japanese name) and a few others. And this makes my Ukemi for them very poor. Everyone has his own weak points.
Here's the problem I have with your statement. I do not consider *any* throw where uke falls solely to save themselves from injury as real aiki. It may be good solid waza, but it's jujutsu kansetsu/nage waza and not aiki. Real aiki, with real kuzushi (not the running around crap you usually see) gives uke just about as much control over their ability to fall or not as a good koshinage (o-goshi or the more classic across the back version in the Aikikai). Aiki waza creates the exact same imbalances in uke and the same dependencies on nage as o-goshi, harai goshi or osoto gari (all throws that could be considered koshinage). Real aiki leaves uke wondering what happened, not a joint strained to the point of failure followed by a heroic leap to safety.
We don't allow many inexperienced folks to train at our dojo, but the couple that have been allowed in, focus on falling from osoto gari, and then o-goshi. Aside from the solo stuff, that's basically all they do for months and months. If you can't take those two basic falls, you will be very limited in what you can study and frankly, they're just not that difficult to learn *if the person throwing you actually knows what they're doing*. I can throw nearly anyone, even someone with no ukemi experience, up to about 250 lbs in koshinage/ogoshi and set them down on the mat in front of me.