There's some interesting things in what
+Zeke+ is saying/proposing. Please don't take it personnal you two. I think that could be a very interesting mod improvement idea for you
xkcon to deepen the story by considering more incomes, for example joining the scribes in each bunker to identify different extremist factions members inside these bunkers, hunt them down or throw them out, acheiving peace by other means or "bartering" your way through some ennemies with a barter skill or charisma check, that, in Tactics, we do not have enough use for. This could even lead to "reverse" missions where you are trying as a kind of saboteur to prevent these factions to acheive their goal to preserve peace.
I don't know much about your mod, I just started it, but for example when I met with a guy near bunker alpha telling me that I could help slaying the infidels or something like that by brigning a holotape to a certain guy, I really wanted NOT to do that, and wished that I would meet that faction again, but this time to stop them instead of helping them.
After playing Tactics maybe 2 or 3 times, it is clear that they wanted to create some kind of parody where you are forced to play the "evil, patriotic army guys". Seeing the game this way, it could make sense that its unofficial expansion kind of "force you" to play evil side quests the same way. But for me to enjoy being part of this, I think it needs to assume a certain degree of irony, self-criticism or include some characters, like in Tactics, that are fondamentally against your views and show it clearly.