Doesn't seems out of place to me.
When you pay attention to details of quests (especially the main one), there is a awful lot of dark things happening (not completely out of place to our world as someone mention, but both are compatible):
-Tri-Tachyon employees are designated by numbers, executive level are always preparing for life-threatening betrayal between eachother
-"clean up missions" by whatever factions on out-core black-ops
-the level of madness at Kanta's Den (combined with suggestions of inbreeding)
-life conditions in Hegemony hives
-the creepiness of everything related to AIs
Those are small details but combined together they paint a quite dark setting. Anyway, I'm marveled by the level of dedication of some modders here. Starship lLegends is already quite flesh out, can't imagine how much time it takes to write all this side quests, interaction dialog and storylines.
Personal opinion: as long as it go to the level of 40k ("In the grimdark darkness of the black depth of a dark future, there is only darkness....") and still connect to the audience it's fine.