The RPG settings are like the cook recipes. The text is the same for everybody, but these cook it in their own way. One can add shadar-kai saying they were survivors from the disaster in Kalidnay, and other can say these aren't wellcome in their game. Somebody can tell in their campaing the Athasian drows were elves slavered by the shadow spiders but they rebeled against these and now they have their own secret underground town. A DM could allow shardminds, a living construct PC race from 4th Ed but with a requirement, the living construct in Athas will suffer an effect like the Disquiet by the Prometheans (White Wolf CoD game)
. Or a player could suggest to use elements from the 3.5 sourcebook "Sandstorm".
And the time travel was canon in AD&D.
Other idea is to start from zero, but using things from different settings, for example an ancient dragon cult created a demiplane, with two secret planar gates to Athas and Jakandor, but these are discovered, and the until now dessert place is being explored and settled by factions from both D&D settings. With a spin-off you can surprise your players without worrying too much with a "jumping the shark" effect.
And Vecna, the lord of the secrets, can find his own reasons to send agents to Athas.