You might not be far enough into the game to unlock all the options yet.
Cerberus in 3 are no different than the Heretic group of Geth in the first Mass Effect or the Collectors in Mass Effect 2. It's kind of weird to navigate sometimes. Reapertech, indoctrination, TIM and Cerberus just being thraws of the reapers and thus get help from them, and 'help' from the refugees at Sanctuary.
But you can load other DLC mods INTO a different DLC mod's folder to combat overriding (I used it to edit the opening outfit but keep using the EGM), so that's always an option if you don't mind experimenting quite a bit. Note about DLC mods: In my experience the Expanded Galaxy mod overrides other mods that edit armor and the cargo deck and what-have-you, even if I'm using separate DLC folders to install the mods. My thought is if the extra armor sets and the map is working then so is the rest. I know it took me a long time to figure out how to change the marine strength, but it was all there, I was just being dumb. When you open your terminal it has 3 options (videos, Spectre, and 'Normandy' I think?) and one of those options (Normandy) has more options in it to customize the crew. Only certain crewmates are eligible for certain positions. Sometimes you'll get an email from a crewmate after you complete X amount of missions about recruiting more NPCs, but you have to assign someone to the position first (Marine Officer, Medical Officer, XO, Gunnery Chief, etc).
