The difference is that many believe that the kind of bot detection algorithms used by chess.com probably can't be made for PS, which means there's no real way to give average players a bot-free ladder experience. It also basically invalidates Smogon's suspect test system for rule updates, which assumes that players who can reach an ELO cutoff have reasonable views on how to improve a format.
There's online tournament cheating potential as well, but from my time in that community it was pretty common knowledge that ghosting by top level human players was just accepted if you were in the right circles.