If you read the bottom of the file, it talks through how the fix works and how you can manually change it to work with specific factions in your load order. It's the best compromise based on how AI and faction relationships work in the engine.
To make sure I understand correctly, in my case I would change:
SetEnemy LETrangerFaction NCRFactionNV 1 1
to
SetAlly LETrangerFaction NCRFactionNV 1 1
Is that right? Or do I change the numbers to zero? Also, just curious what type of mods you think might be causing the conflict in the first place? Thanks again, I appreciate the help.