I am keeping the details of these quests as intentionally spoiler free as possible. Please keep that in mind as you comment.   
 

In the Quest Trade Secrets, I can resolve the quest to favor Delver's row. I get a point in Benevolent despite never taking dialogue options for it. 

In the Quest Coming to Terms, the same thing happens if I resolve in favor of the Duape. 

I am almost certain there are other quest triggers like this. I am not sure if they raise other reps than Benevolent.

 

Now, the trouble is, my Watcher is not some noble altruist;

In the former case, He's trying to ensure continued supply of contraband and information, mainly for himself.

In the latter case, He's trying to screw the Valians over, and maybe catch a reward for doing so. 
 

I'm not asking for the game to keep track and cater to every possible player motivation. That's ridiculous and improbable.

But it would be good if it could recognize that motives are complex, and not award reputation for resolutions, only actual behavior. 
 

Edited June 14, 20187 yr by Parasol_Syndicate

Yes, certain quests give you unwanted dispositions, no matter of your choice during dialogue. It is annoying.