Have to say I didn't encounter many wtf ones.
All my colonies prosper. Doloroso's Druisian cult grows huge and wrathful after his repentance walk, Explorators also huge.
Footfall got ♥♥♥♥ on because I side with Chorda and don't support the Kaballistica. Octavania decides to rat them out and becomes a REAL bartender.
Dargonus kinda replaces Footfall to become the main attraction while Vearboo II for the criminal/underside.
Janus becomes a shelter, and the eldar there remain BFF, with Muaran.
The drukhari are ♥♥♥♥♥♥ hard by Chaos daemons that they aren't bothering to raid us.
For treating Necron warrior with respect, somehow they don't attack my ships.
The local Chaos Cult ultimately exterminated, Word Bearers retreated back to their craphole.
Almost all of my companions got glorious ending, with the most badass one being:
1. Argenta becoming some sort of Grail guardian for the Relic after kicking ass sort of ass, waiting for the next pure of heart.
2. Ulfar becomes sort of immortal loner wolf hunter that kills Chaos and the wicked. He always survives.
3. Pascal starts a huge crusade on Dark Mechanicus and disappears. Abel stays with him and enjoys being the Imagination component.
4. Cassie my love becomes the Novator and rules the house nobly, we still exchange letters but she decides to have heirs.
5. Heinrix becomes the new Lord Inquisitor, trained thousands of disciples and fanatics under his name until he dies during the line of duty.
6. Even minor character like Macharius Sauerback becomes my BFF due to my exposing his wife's indecency.
The only wtf is Yrliet I guess, she stayed with the RT for many years until she goes over and get killed by Pascal.
And I become the Warden of the Expanse with thousands of pious men chanting my name, and I unironically make the Koronus Expanse less of a space for Rogue Traders. But that's for the better, no?
Verdict: 10/10, not grimdark enough I guess.