Even if they use the "new cosmology" of the "assumed setting" there's nothing at all that suggests there's only one pantheon. They never specified the number of Gods there really were, beyond the number they put in the PHB strictly for player options, and nothing to do about their world.
Multiple pantheons can exist just fine without the Great Wheel, and it will greatly benefit Planescape if death was left a mystery, rather than the stated Absolute Truth that, "everyone who dies becomes a petitioner to a plane of their appropriate alignment." Instead that previous statement could end up becoming one of the truths that only some believe, while everyone else thinks something else happens and may indeed be right.