There's already an implication of a new adversary within Shadowbringers' own climax.
Something caused the Amaurotians' powers to go haywire. A Sound from within the planet led to the creation of the First Doom, and began a cascade of terror that heralded the end of a world.
In classical Final Fantasy fashion: "Oh, these obvious villains you've been fighting since day 1? They're actually extremists pushing back against something much worse, and the rest of the world is just caught in the middle. Since you killed them all, that enemy is now unopposed, setting up the true final boss. Nice Job Breaking It, Hero."
I'm not sure we'll be fighting Lavos specifically (since 14 is a celebration of the entire FF series and Chrono Trigger is just a bit outside that purview)... but that is an interesting theory.
That said, I expect the core of 5.3 will be about wrapping up our involvement in Norvrandt more than dealing with the Ascians themselves. No doubt that we'll fight him again, but to just kill off Elidibus now would feel like kind of a hasty wrap-up on a multi-expansion arc (and extremely soon after Emet-Selch), particularly given how Stormblood was a drought for Ascian content and we've only just learned their motivations.
Besides, Yoshi-P said we wouldn't guess who the trial boss is, and Elidibus is easily the most obvious choice for a big wrap-up trial.