So my question is not how NPCs react to monstrous henchmen specifically - but rather how they would react if, say, a Thrassian was in the party, but the face man was the one causing a reaction roll. If trying to talk to the leader of a town, even if you're trained and supernaturally charismatic, would you take any penalties if you have a hulking monstrosity armed to the teeth(and beyond, in this case)? Would the penalty to reaction rolls from the Thrassian being widely feared and reviled(as his racial ability) apply to the face's reaction roll? I personally feel that there should be some kind of penalty involved but I'd like to hear how others(and hopefully the Autarchs) handle it.
Not an Autarch, but I'll weigh in: Reaction rolls can be a bit of a tricky beast in this regard. I have run into something somewhat similar: the person who wants to be the face, with their improved charisma and proficiencies that boost diplomacy, doesn't speak the language of the people they're trying to interact with. I had to come up with something that felt fair when allowing a translator, which was that the face being translated for can't have more than +2 higher than the bonus/penalty the translator has.
For your issue, I think the logical choice is to let the person being the face use their modifiers. Consider: would you allow one person with diplomacy, one person with mystic aura, and one person with +2 Charisma mod to combine into a massive +6? Similarly, you probably wouldn't stack all your penalties. More likely, you would apply a one time modifier, possibly equal to the Thrassian's penalty, if that particular npc had some beef with Thrassians that was noteworthy. Of course, if you opt for it to be a common sentiment, be prepared for the party to come up with circumventions, such as putting the Thrassian in cloaks and hiding them in the wagon when it's time to talk.
Regardless, now is a good time to revisit an important thing to remember about reaction rolls, something I often fail to remember myself in the heat of the moment or in a dryspell of inspiration. Remember: for most rolls, the result of your reaction roll is just the blurb on the dust jacket telling you why you should buy the book. It tells you what's at stake and how dire of a situation the heroes find themselves in, but it doesn't tell you how it ends. That's up to the players and how they choose to roleplay. It's not to say that clever thinking can 100% of the time turn foes into friends, but someone who comes into an encounter respecting that the other side is hostile should be able to use a combination of puffery and de-escalation to avoid a confrontation if that's what they want to achieve and they probably pick up on the cues of what the other side values.
I am not an Autarch (just some guy - PS quit stealing my name :P).
Personally, the way I handle this kind of thing is to apply half the penalty (rounded down) in cases where something objectionable is in the party but not the face. (So with only a -1 penalty, it rounds down to zero.)
I don’t do the same for bonuses because bonuses generally require actual interaction to show their nature. If the bonus came from its sheer nature (like having an angel follow you around or something), I very well might give half the bonus, but in that case I’d be more inclined to just design the angel abilities around knowing that it’s not the face and say that it gives +X to reaction rolls while it’s with the party even if not interacting.