Honestly, the question belonged here, rather than in the Starship Legends discussion thread, so here goes: At any point in this mod's history, was reputation gain tied to a battle's difficulty rating and NOT experience points and/or levels gained?
I have a vague recollection from 1-2 years back that even though my player character's + officers' levels were all at least 10 (raised the limit on 'officerMaxLevel' to 15 in settings.json) that I regularly got double-digit rep gain from winning lopsided battles (that is, I was outnumbered)...
...that is, until updating to v1.3.0 of this mod and/or updating Nexerelin to its own latest version (which come to think of it, might have its own internal mechanisms that control reputation gain between the different factions it has to handle, but I can't be entirely sure of that).
EDIT: As further evidence that I have little idea how the increased reputation gain is supposed to work... after a fight against a large Remnant Ordo, I did get the expected reputation gain, but not when doing Bounty Board missions (implemented via MagicLib).