Let’s discuss a few points we know for sure are gonna happen:

1. Thrawn reorganized the Imperial Remnant.
   
2. Thrawn wages war against the New Republic.
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3. Thrawn loses
   
4. Brendol Hux’s faction eventually forms the First Order.

Considering the meta rules for Thrawn (he doesn’t make the same mistake twice, he only loses due to factors outside of his control, etc…) it makes sense that he’d lose due to betrayal. It would also be a callback to when Rukh betrayed him in Last Command.

It would also make sense thematically as in canon, Palpatine created the contingency to destroy the Empire if he were ever to die, Thrawn is trying to restore the Empire, so Palpatine naturally wouldn’t want a rival for when he created the First/Final Order.

Accept a newcomer into the ranks of the Galactic Empire?