I don't really have an idea of the events regarding Trench and why he was still director prior to Jesse arriving and her becoming director, but I think Trench shooting himself right when Jesse gets to his office hints at some manipulation by the Board through the service weapon.
Right when Jesse picks up the service weapon, and shortly after, we get some background info about it and how it decides whether the user is "worthy." This seems to me that the Board is the arbiter of who is worthy and decides, through the tests in the Astral Plane, who can use it. Also, it seems pretty clear to me that the containment breach that lead to the lock down is the projector being used to allow the Hiss through. Dylan and the Altered Items are secondary breaches.
So, I see it one of two ways.
Trench is still director when Jesse arrives at the FBC because there were no "good" candidates for director available until Jesse arrived. The Board would probably be somehow aware of this. It's possible that the Board felt having any director is better than no director and kept him until the situation presented itself where they could replace him. Jesse appears and Trench kills himself with the service weapon. Jesse becomes the director and the rest of the game follows.
The other way I can see it is that Trench was at the end of his usefulness to the Hiss and they saw a potential to accomplish their aims using a new, inexperienced director, Jesse. They do try to take over Jesse shortly after she picks up the service weapon but they fail. It's unclear to me whether or not Dylan has escaped before Jesse arrives at the bureau or if he is still contained and escapes at some point prior to Jesse arriving at Containment. It's also unclear how long the lock down has been in effect prior to Jess arriving at the bureau. Anyway, it seems Dylan has some control over the Hiss and isn't like the mindless enemies you fight throughout the game. The Hiss probably feel they can manipulate Jesse through the use of Dylan and that is why he surrenders when he does.
Personally, I don't mind that it is unclear what the exact situation is. Kinda fits in with the background themes of the game. I don't care whether or not that was intentional.
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