Oh gosh, I know. He states it as a fact, like he's absolutely sure of it, and he must have been told how annoying or weird or out of place he is before, likely from multiple sources to say it so matter-of-fact. He's heard it enough that it is now truth, across the board: he annoys people.

And as you said, at least now more people have heard of autism, while back then people tended to view mental illness as a reason to lock someone up and throw away the key. In present day, even if they don't understand it, more people are at least willing to give the behavior a pass. Back then? Newt obviously manages to function and take care of himself (and all of his creatures), but there are still so many things people would give him such a hard time for

Lack of eye contact/shying away from physical contact? Rude.
Special interest in animals/magizoology? Weird.
Infodumping about said special interest? Annoying.
Difficulty dealing with too much stimuli? Too sensitive.
Hyperfocus/tuning everything else out? Probably not that bright.
Stimming/excitement/disproportionate emotional responses? Childish.

I mean, I could go on. But that's why I particularly liked your point of adding Theseus in and having him understand; if there's even just one person on your side, then that's something. There is at least one built-in person who knows Newt and accepts him as he is. Plus sibling/family fluff is kind of a favorite of mine. Plus-plus, if Graves really is as brusque and businesslike as he's shown to be in the film (presuming Grindelwald at least attempted to approximate Graves' behavior so he could pass for him), it might take someone else pointing out "maybe you need to look a little harder" before he realizes Newt isn't just being a general clueless irritation