Here are my thoughts, having reread the big post:

Is it “months earlier”? TCW covers about two and a half years, and you’ve got Eminence about halfway through the show. Then again, there’s definite a time jump between the original six seasons and the revival episodes (as made apparent in Anakin’s hair and Ahsoka’s deisgn), so “years earlier” would imply too much time. Wookieepedia has Christophsis in 22 BBY and Eminence in 19 BBY, which surprised me.
My vote is to keep the Domino Squad arc together, even if it means using cheap tricks like “MANY MONTHS LATER” titlecards between the three episodes or something. Helps you remember who’s who in Domino Squad, IMO. It’s definitely an odd one, because ultimately Rookies is a fairly decent early episode for establishing Rex and the Clones, while iirc Clone Cadets is more of a set up for ARC Troopers than for Rookies itself. Having two adjacent Season 3 episodes act as a prequel and then a sequel to an episode from two seasons ago has got to be one of the most early-TCWy things in early TCW. Then again, Echo and Fives go on to be very important pretty much right at the end of the series, so having so much of their stories be told so early may actually cause a theoretical audience to have forgotten who they are by the time the Citadel, Umbara, Biochip Conspiracy and Bad Batch arcs come around… Perhaps you could alternatively just keep Rookies separate, early on in the show, then combine Clone Cadets and ARC Troopers with Clone Cadets being clearly framed as some kind of flashback before ARC Troopers. That lines up with how the episodes were released.
Your season 1 and 2 seem like a lot of fun, which is surprising considering the original first two seasons of this show.
With The Deserter, could it make any sense at all to combine it with the Gregor bit of the Void arc? Cut is a Clone Trooper who doesn’t want to be, whereas Gregor rediscovers that he’s a Clone Commando and embraces it, so there’s some thematic potential. That or just leave the B-plot in. Your plan to concentrate Rex’s development in the latter half of the show seems wise to me, though.
Trimming Onderon is definitely a good idea. I remember feeling that arc dragged when I first watched the show.
Any excuse to include the excellent Anakin/Obi-Wan conversation from the Utapau arc is good in my book.
It’s a shame that Bad Batch uses the updated Anakin model and thus is forced so late because it doesn’t feel particularly tense or important.
I don’t recall Ventress’ bounter hunter chronology well enough to really comment on the changes. I wouldn’t be super concerned about Boba being soft though, because we see in Mando that he’s a fairly chill guy with a moral code of some kind, even if he has done some dirty work for Darth Vader and Jabba in the past.