Something about the chronology still bugs me, so I went back and re-watched the Shadow Council scene in 'The Spies' to refresh my memory, and while it's not concrete, it does seem as though there's a reasonable case to be made for Thrawn already being back by that point, and by extension, all of this show happening before Mando Season 3;
Observe.
Of particular note is this exchange: -
This could be taken either way of course, but it would make sense that once back, Thrawn would want some time to establish himself, keep a low profile, and get the lay of the galaxy before making moves. It's not like him to just come out swinging.
Indeed given what's being set-up, I suspect we'll see Hera removed from command, and the New Republic remain wilfully ignorant of Thrawn's return for now. Though the implication there could be that Ezra never actually makes it back home, since it'd be pretty hard to deny the narrative when the person last seen with Thrawn reappears.
Yes Gideon says he's heard no whispers despite him being Mr Head Spymaster Person, but he also says he's not doing any cloning work, so we know he's full of crap and what he says here cannot be taken at face value. It's entirely possible he knows full well Thrawn is back; meaning that's partly what's driving his need for his force adept super-clones, and why he's posturing so much to gain as much sway of the council as possible before Thrawn shows his hand.
