And then I assume this message also goes out to the other Final Order ships (since it reaches all the First Order ships across the galaxy), which means the whole civilian fleet would also be shooting down ships full of these newly unbrainwashed troopers, killing them all without a second thought.
Nah, Sith troopers are a different breed entirely. They’ve basically been raised in a religious cult and have only seen the grey skies of Exegol. Whereas FO stormtroopers have seen countless worlds and scenarios that could help them shake off their conditioning.