I'm enjoying the book a lot as I go through it; some of the new characters on DS9, particularly the new security chief, are very interesting. Rogeiro also gets a bit more to do this time.
As for Geordi, the novel says having two captains wasn't an ideal situation. Anyway, Indistinguishable from Magic sort of put all the toys back in the box at the end.
Like I said, rank does not always denote postion with a command structure, IDM even with out of the way to expain the captian of engineering part , and How it fitted into the over all command strucure, so them to reverse that served no real logical sense, other than they just wanted to