It sounds like you’ve been amazing and incredibly thoughtful to your son, he’s very lucky to have you as parents.
My feeling (and it would be interesting to hear what others think) is that there could be some more consideration from your son here.
Your daughter doesn’t have misophonia and isn’t doing anything wrong by eating crisps from time to time. Misophonia is tough on your son, but it will also be difficult for her and for you and your partner. It’s a cruel disorder but none of you should have to feel like prisoners in your own home.
I think it’s about balance. If someone’s purposefully goading him and trying to trigger his misophonia then that should obviously be clamped down on. In other situations it sounds like there could be more awareness from his side. Ultimately he is the one with the disorder (not the rest of the family) so he needs to be willing to make adaptations too.
If he’s feeling triggered he can leave the room or take a time out. Otherwise if everybody is treading on eggshells around him the whole time it could lead to a very tense/anxious family environment.
The ideal scenario (easier said than done!) is being mindful and forgiving of one another. Maybe being aware that if he shoots a glare from time to time, it probably isn’t him, it’s the misophonia being triggered. Carrots, crisps, apples… are like foghorns to misophones so maybe try, where possible, not to be right up in his face doing it (not that it sounds like any of you are). By the same token if comes into a room where someone’s eating it’s no big deal, he can go somewhere else for a bit.
When he gets a job and/or leaves home one day he won’t be extended the kinds of courtesies that he’s had at home by strangers or colleagues. It will help him in the long run to work on his own coping mechanisms. If he can do that, he can take on the world.
I hope this helps.