I don’t know when the whole OCN->IP->IN thing started but I would guess shortly during or after the silent era. At the beginning, all prints were made from the negative but I’m sure they’d had to have learned their lesson after a couple of years…
I would say that the difference between SW/Godfather and their sequels is the fact that these films’ popularity exploded. They probably didn’t think they would be the massive hits they were and didn’t think to take extra precautions to create enough back ups.
They had learned their lesson by the time Empire and Godfather 2 came out.
I too am curious about the workflow of Super35 (and techniscope for that matter). I have no personal experience with either format. Nowadays, it’s easy: everything is scanned.