I now have a better understanding of what happened. The W116 was originally designed to have different door seals than what most of them have. If you look at the profile of a 1960s Mercedes door seal, they look a bit like an "eyelash", which fits flat against the side of the door opening when the door is shut. When they designed the W116, they originally had round, hollow profile door seals which, instead of sealing against a flat surface, were design to seal against the corner of the door opening and crush to conform and seal from two surfaces.
However, for whatever reason, only the very early W116s had these door seals and they were abandoned and replaced with the old style "eyelash" seals that are designed to rest against one flat surface of the door opening. However, the door opening doesn't really have enough flat surface area for these to work, so they had to make the seals oversized and stick out past the edges of the doors just so they would seal at all. However, this had the consequence of the front door seals rubbing on the rear doors when opening and closing.
This is a true oversight/mistake by Mercedes engineers. They designed the body to work with a different door seal than what they ended up using after a few cars were made. The body would need to be redesigned so the door seals most of our cars have (and the only ones currently on the market) would work without rubbing on the rear doors, and it would have cost too much money.
Even though the W116 is largely sorted out in terms of engineering, there were a few instances where it was awkward and failed. This is one of them.