I could swear the update file overwrite was fixed for a while, but it seems to be back now! Sorry if you haven't actually looked at it yet, I might be imagining things...
On another note, I had a thought about the old gimp <-> G'MIC zero opacity handling bug. Instead of trying to deal with the output not being written in fully transparent areas, it might be better to always "sanitise" the input when previously transparent regions might be revealed.
Example: with -remove_opacity, set other channels to 0 where the opacity was 0 beforehand.
Another choice is to do that automatically with every gimp input: where opacity = 0, set all channels to 0. There are downsides to that though and it's a relatively rare problem.
Of course all this would be moot if they just fixed the actual bug