That doesn't mean they missed the joke. There are a number of reasons they might be acting like that, you don't get to choose which is the correct one.
Nor do you. That's the point.
Since we can't read the NPC's mind, we'll never really know why he reacted as he did.
But it also doesn't matter what conclusions you draw. It only matters if your character draws conclusions about the NPC. Our characters fan use whatever standard of evidence or mode of reasoning we want, and I can't imagine they would ever think that the NPC's reaction was based on the intent of the writers (who don't even exist from the character's perspective).
It makes their behaviour inconsistent. If we assume that there is no writers and thus no intent of tone, then there becomes no discernible pattern as to Alistair's behaviour when I assume an insulting tone of what the writers intended as a joke line because eventually I'm going to start hitting upon dialogue options the writers did intend as insults and he's going to react differently to those.
Just like when dealing with real people. Isn't that the goal?
Even as much time as you spend with him in Origins is enough time to start seeing the patterns, unless you break the character by assuming random tones of dialogue.
I am not Bertrand Russell's inductivist turkey. We learn things about the characters only when we fail to predict their behaviour.
I said all we have to go on is their reactions, and their reactions aren't being consistent when we get to choose any random tone of voice that we so desire because the game always plays it like you used a very specific tone.
We can't tell their mind but we can discern patterns in behaviour, as everybody has them. Anybody who was 100% unpredictable would not be able to hold a normal conversation.
This happens for me just as often with the voiced protagonist, so I don't see how this is an argument against the silent protagonist.
And again, it doesn't matter whether we can. What matters is whether the character you're playing thinks the NPC is inconsistent. And this happens for me all the time, voiced or not.
I mean I don't know your mind, but I do know with a decent level of certainty that you're going to continue your personal crusade for turning Mass Effect into your very specific definition of a RPG. If you ever stopped doing that, it would be inconsistent with your behaviour.
I find this observation very amusing, as you've misidentified my objective.