Faction reaction loading is incorrect
Faction reactions in the ESM format are pairs of other faction id, multiplier
with each pair being a subrecord. A faction A can have multiple reactions to the another faction B. Morrowind.esm gives us this gem:
In Morrowind.exe this is a non issue, an NPC's reaction multiplier is the lowest reaction for any factions the player is a member of. Using the faction above, that means Ashlander players get a reaction of -3 and Census and Excise players a reaction of -1. OpenMW on the other hand, squashes the reaction list into a map, causing the last value in the file to be chosen, leading to both factions getting a reaction of -1.
I guess it also means OpenMW-CS is incapable of saving Morrowind.esm without changes. Though I'd argue deduplicating reactions is a feature... It just needs to select the lower value when it encounters a duplicate.