There's a very valid reason why you don't just turn off your computer by yanking the plug out of the wall socket - and flipping the PSU switch is the equivalent of doing that. Do that to your desktop computer a few times and see how well it runs as a result...
Yeah I have turned PC off GPU rigs at the switch a couple thousand times. It is a non-issue. There is a reason open frame GPU miners used power supplies with a physical power switch on back.
you missed the whole point, the motherboard being hooked up properly with those pins tells give the PSU a reference as to what to do and that its ready to shut things down instead of POP powers gone.
Regardless of the 2 pins that are shorted, the other voltages drain into the motherboard after it's turned off.