@JayarrI don't know anything about mapping and how hard this is or what not, but seeing as you said only stuff inside base (besides the 2 exceptions) are brushes how would this idea be:
Removing this room and pushing that blastdoor upto where the doorframe is currently (see next few pics and my amazingly drawn door)
Room I am talking about ^
New door ^
With that, remove the current armory and place it in this hallway so it has a purpose, like the pics amazingly show below:
Armory ^
No armory ^
With that, also deleting this area above brig:
Above brig^
And place the citadel here, or wherever it is best to place:
Would love the feedback on this idea as it just crossed my and another player's mind.