How potentialy damaging is it, setting bit 6 of $2000? Should I be worried of homebrews from newbies ? Or forgetting to turn off a gamegenie code from one game to the next with my everdrive n8 ?
Theoretically it's possible that it might blow out the n-MOSFET pull-up drivers that're on the expansion port. But since these pins will never be used for anything unless you install something that uses them, you probably don't care.
I have to think that if Nintendo actually had been concerned about damaging the PPU they'd've put resistors to ground on the lines rather than simply tying them low.
I have not seen the PCB, but maybe it would be possible to put the resistors yourself. Another thing that would be possible is emulator to warn about PPU slave mode, but I don't know any emulator that can do this currently.