I wonder what was the issue that required a total replacement / total repair of the gearbox?

For such mileage, it has to be extensive damage.

True.

I don't think issues like delay or jerking would need a total replacement of the gearbox or extensive repairs.

It has to almost certainly be mechanical or physical damage to the whole transmission component.

At this point it almost feels like Proton gave a total sure-fire but expensive strategy to fix a problem.