Before anyone thinks I am focusing on Saotome, let me just make clear that all of the "uchi-deshi" (kayoi-deshi?) in Hombu from about 1955 to 1969 got far less hands-on time with Morihei than aikidoka in the West would expect from the term "live-in disciple." And the Japanese who stayed in Japan like S Endo are quite frank that they didn't train all that much with Morihei. Their major influences were men like Tohei and K Osawa. They took uke for Morihei a few times, heated his bathwater, etc. But Saotome's and Endo's value to us today has nothing to do with how much hands-on time they spent with Morihei. It's only in the West where people take this "I trained daily with the Founder" material seriously. You don't need to have trained with Morihei daily to become for instance, an Endo or Saotome.
I think Endo Sensei isn't the best example, though - when I have seen him he has stated quite clearly that he regards Yamaguchi Sensei as his main teacher.
All the same, he was very much part of the "establishment" in the Kisshomaru era - there is plenty of footage out there of him taking ukemi from 2nd Doshu.