Ah yes, I'm glad you brought this oop. I've been meaning to discuss his potential status as "Anti-hero"... or straight up "double agent."
For sure, Thrawn would make for a perfect "Big Bad" vs teh Mando'z & alliez... but what's teh point? The Empire is dis-empowered already. I've alwayz felt like he would double cross the empire at a crutial moment anyway.
Though teh Chiss had conflicting government at timez, they just want to be left alone to do what they do. They regretted expanding their reach into teh Jedi/Sith warz 1,000 yearz ago... & only just recently expanded their reach beyond their boarders "to detect a potential threat." Their objective is not dominance of others... but sovereignty within themselves, and I think that's Thrawn's end game dispite any local turmoil within his own people's bureaucracy.
iow...
Thrawn's not with the Empire because he thinks the Empire is his end game. That said, he could use his position to head the empire & then double cross them at a key moment. The Chiss had a mandate "not to strike first." They don't want to be involved. They just "scouted" the Empire because they saw the threat. This seems like a perfect opportunity to lead the remnants of the empire into a war they can't win & then pull the plug & split.
On a more personal level... the Chiss deal in "respect" above all else... and so align with those capable of keeping their promises. That's at "religious levelz" for teh Chiss.
I find it obvious that Thrawn's long time dealingz wit teh Empire have offered him enough examplez to question if the empire would break their promisez & try to take over teh Chiss community. (spoiler: "of coarse they would") That's obviously the highest order of disrespect... which goes against teh long-standing Chiss religion... their way of life etc... etc... etc... It goes against every single thing teh Chiss have developed for as long as public record can recognize, and seemingly against what Thrawn himself strives for. He went in for intell to see if teh Empire would leave them be... but he would almost have to be BY DEFINITION... "anti-empire" at this point in time, yeah?
I'm just throwing out there that Thrawn'z sabbatical with Ezra might show him a more dedicated allegiance that is more worthy of teh Chiss beliefs.
PEOPLE OF HONOR... like teh Mando's who share teh Chiss belief of honor & keeping your word would be his most suitable allies. in teh Mando'z. The mando'z once rooled over 1,000 planets, and are in a major hyperspace lane... so I'm sure teh Chiss are well aware of them.
So the re-taking of Mandalore could come down to one simple command from Thrawn which is designed to fail the empire from the inside, and now he's got permanent & trustworthy honorable allies for life in teh Mando'z. Big hugz all around yeah? Just don't remove your fooking helmet.
By the current timeline... the Empire is gone & Sid dis-empowered, so I don't see why Thrawn would be pro-empire. It serves no purpose.
Maybe Thrawn has his own agenda, but he seemz like a good guy to me at heart just out to protect his own people & do what's best for his civilization. It was only a matter of time before the Empire started infringing on the Chiss too, and so that was Thrawn's original objective in joining them.
There is no allegiance to the Chiss outside of Chiss Sovereignty. They will fight only to dissolve a threat to their sovereignty. Thrawn could effectively just go home & see how it all shakes out at this point... lol...