There are two sides to this coin.
I don't agree that you simply shouldn't feel offended or hurt when he snaps at you. We ALL have a responsibility to learn how to communicate effectively, use tact, and generally be kind and sensitive to others, though that responsibility is VERY relative to situation. But when it's a significant other, there is a top priority there.
Have you tried opening up a channel of communication with him about these things? I think it's wonderful that you're striving to understand him and be respectful of his natural aversions and disposition. He, likewise, should strive to do the same.
I like to share input in the form of personal experience, so here we go. I have a few quirks like this. The sound of my father's chewing boils my blood. If we're eating together I will either wait until he's done, or I will serve myself first, inhale my food, and excuse myself before he starts eating. I CANNOT cope with the sound. My blood pressure shoots up, I feel angry, and every fiber of my being screams "Make the sound stop" and it's very hard to remain calm and relaxed. This isn't much of a problem though, considering I've been moved out for nearly a decade and don't feel subjected to it anymore. I will note that I never said anything to him, never lost my marbles or anything. He can't change the INSANE NOISES his mouth makes while eating, so it's my job to remove myself from the annoyance, not try and make others bend to my aversions.
Another example is the sloppy slurping sound dogs make when licking their lips. I love my dogs. I love my animals. But THAT SOUND. And now I've got a 130lb mastiff in my life who not only has to constantly re-adjust his lips and seems like he sometimes swallows his tongue, but also loves to give himself a good slupr-tastic licking that can last for minutes. My heartrate spikes, my muscles jump, my chest tightens, and I have to just breathe through it. I can't get upset at a dog for being a dog, I have to learn how to cope with it successfully, that is MY responsibility. It is NOT okay to take it out on someone or something, even if the agitation is pushing you to the edge.
An example of a person-to-person sound annoyance/aversion; when I'm extremely tired or focused I get very agitated when people talk to me. Some people get chattier when they get tired. My unconscious thought is "can't you see I'm busy/not in the mood? Would you stop already?"
I bunch up physically and wait for them to PLEASE STOP, getting more and more tense. But I get better and better about reversing myself and making myself communicate; because I know to indulge in the tension will lead to anxiety, panic, catatonia, dissociation, or some other meltdown. And I don't like going there.
When my partner is "pestering" me (which he has no way of knowing that his normal behavior is suddenly bothersome to me at this moment), I do my best to communicate. Sometimes it comes across snappy- when I realize that I apologize because I don't want to take it out on anyone and I regret doing so. However, I can find it difficult to explain what's going on. I wish people would take my words literally, not look for meaning in them. When I say "This is irking me right now, please stop. Normally it's fine, it's just right now I can't deal with it" They take that to mean "Never do this again", which I TRIED REALLY HARD to convey that that's NOT what I'm saying. I'm still trying to find ways of explaining what's happening effectively...
I can be extra sensitive when I'm over tired. I think that's common. I don't want to talk or think or engage, I want to close my eyes and SLEEP. And when other people are involved, sometimes they get "in the way" of that goal.
Sometimes it's not even "that one noise" or something predictable. Sometimes I'm just so worn down that EVERYTHING is going to annoy me. Some nights the sound of the wind, or of cars, the sound of rain, or the dogs snoring- or sometimes even my OWN BREATHING annoy the crud out of me and get me grinding my teeth. If it's really bad (which is rare) I wear ear plugs to bed and it's like heaven- the most amazing thing to have ever happened. Silence.
The most common annoyances are dripping noises (I developed that after having a leaky roof for 3 years, now my blood pressure shoots up when I hear dripping water in the house). Rhythmic sounds like clocks, drips, taps, etc. Non-rhythmic noises like cars, wind, or other constant but erratic noises. Rumbling, buzzing, or electronic noises. SNORING (though I try to retrain my thoughts; "awe, the snoring means their having a good, fulfilling, much deserved sleep and I'm happy for them", which usually doesn't work but it calms me down trying to see it in a different perspective). Smells that shouldn't be there, or other sensory indications that my environment is not as it should be. Warm air on my face. Air movement on my face (fan, breath, or wind) <- especially breath on my face! Constant fidgeting of people or animals in the room when I'm trying to go to sleep (which is hypocritical since I'm the queen of fidgets). When I'm feeling extra sensitive and multiple factor compound, it can be hard to think clearly and not just react to them.
I think it's admirable that you're working with him and accommodating!
But it has to work both ways. Your pain is not invalid, and his sensitivities do not cancel out your sensitivities. Work together on this. Encourage him to communicate, encourage a compassionate exchange, and mutually come up with some "key words" (something he can do or say to let you know easily and urgently that something needs to STOP NOW) and some escape plans; ear plugs, a safe, quiet room, etc.
