unknown iff isn't an issue
freelancer iff would have the same effect if you're friendy with the npc faction, which corsairs back in the "raid gamma everyday" age of disco complained a lot about because it was hard for them to tell who was hostile and you couldn't exactly turn hostile to the freelancer faction
so ye the only real problem is that he docked in the base of a faction he had just shot at, everything else sounds like you're jealous and could be replicated extremely easily without unknown iff (and in fact replicates regularly with freelancers who are red to the people they bountyhunt but aren't red for the people they kill)
