Specifically I am interested to know which muscles Osensei is in danger of micro-tearing or overstretching as a result of the specific stretching pictured above.
In the bottom picture, pretty much every muscle along the back of the leg, from the Achilles tendon all the way up to the glutes. Possibly lower and mid-back. Every muscle that you can feel in a stretch is vulnerable to damage if the stretch is performed improperly.
Obviously, from a static image it is impossible to say what O Sensei was doing internally or what preparatory movements he had done. I'm certainly not going to claim that he was doing it "wrong." But I also suspect that the vast majority of aikidoka who perform that stretch don't have the foggiest idea what O Sensei was doing, or what the "proper" "aiki" approach to that exercise should be. Without that "aiki" content, they are no different from any other athletes, and research on other athletes shows pretty definitively that "non-aiki" static stretching before a workout is a bad idea.
"Because O Sensei did it" isn't a bad place to begin one's explorations, provided you know what "it" actually is.