I can't comment for the other person (people), but when I remove an FMJ wiper transmission assembly to replace the bushings, I will remove the short arm from the wiper motor (leaving the wiper motor in place) and both wiper pivots - as an assembly (or pieces depending on condition of bushings).
Then I take a sharpie and make a line, or dot, on the front edge of Left side of both metal arms. I do that because the arms will get moved around a lot getting bushings off and back on again - and sometimes i don't remember how the arm came off when re-assembling. A quick mark solves that problem and sense it is deep inside the cowl, you can't see the paint marks when re-assembled.
Getting those bushings re-popped back into place takes a bit of effort to do, so I highly recommend attaching the wiper motor arm onto the bushing before putting the transmission back into the cowl.
I still can't picture how or why the nut is doing what it is doing - for as many wiper motors and transmissions I have manhandled (at least 200) I haven't experienced this to be a problem before, so unsure as to what to say.
BudW