I find that it actually does have a lot of those things, to some extent of another.However, in this book, the presentation of the Realm's government hearkens back to that 2e style of worldbuilding. It is corrupt and dysfunctional, but it never feels out of control. You don't get a lot of blurring of boundaries, unintended consequences, or loose ends. The Empress wanted an empire that only barely worked and that's what she got. I'd have liked to see more stuff that felt like an organic growth out of a living history. Personal fiefdoms carved out despite the Empress' suspicions, atavisms that never quite got wiped out, concessions to peasants inelegantly disguised as something intentional, and criminal syndicates not run by the Great Houses.
It's not wrong for it to lack all of them. Successfully preventing Great Houses from having exerted too much territorial independence, for instance, is not only the kind of thing that some actual empires have managed, but can serve as a point of tension driving the motives of characters in the course of actual games.
When the thematic underpinning of the game is being in a setting in which the centre cannot hold, it's kind of necessary that people are used to the centre holding in some fashion. There's a degree to which these things need to be designed according to theme, tone, and being an engine for playing games and telling stories, rather than fully simulating an entirely realistic world to talk about.
Also, two whole Great Houses carved out a fief for themselves in the Southeast that the Realm tries to save face with by calling them cadet Houses and their empire a satrapy, so it actually does kind of have all the things you're asking after.
For the sorcerer stuff, I think you need to meet them halfway a bit; I don't find it reasonable to want them to filter out every possible thing that is reminiscent of stuff that people might have baggage about. Stuff with Bagrash Kol and the Eye is implicit in the fact that basically no magical item in the setting is capable of operating itself, nor do they have simple on switches.