Well I think the "Pun-Pun plugged into J Random Setting" thing won't work.
If gods were as powerful as to forsee Pun-Pun, then one of them would be sure to create the Sarrukh race in the first place and make himself Pun-Pun. Any time any god detects Pun-Pun on his "future radar", Pun-Pun will be created (one way or another).
If they are not that powerful, then they are probably screwed. Pun-Pun works in (I think) 4 rounds "normal time".
Thus, I'm fairly certain that Pun-Pun exists as long as the Manipulate Form ability and "scaled ones of toril" exist in the same setting. Thus, time is pre-empted by Pun-Pun. Thus, he pre-empts any and all settings. Thus, everything that happens follows Pun-Puns will. If another Pun-Pun were to arise, it would be with Pun-Pun's consent.
In campaigns, I'd usually define Pun-Pun as something much larger than the entire setting. If each setting is something on the scale of a meteoroid to a planet, Pun-Pun is on the scale of the universe. Thus, for most intents and purposes, Pun-Pun is irrelevant to the setting. Which tends to be the case in most games that are actually played. I'm aware that Phaedrus is playing "Pun-Pun" (i.e. his interpretation of Pun-Pun) in a campaign right now, though.