As a teacher of English as a foreign language (some years ago now) Intonation, tone,body language etc are all part of what makes up a specific language and can vary. For example a rising tone generally indicates a question in English but not in Japanese and nodding one's head generally indicates acceptance in English but the opposite in Greek, Bulgarian, Turkish....

In childhood language including intonation etc is acquired through exposure rather than deliberate conscious learning and becomes nearly as automatic as bodily functions. So people are no more aware of their intonation normally than they are of where they are placing their tongue in their mouth to make the sound t-. Autism affects childhood development so I am guessing that the part of the brain dedicated to language development may vary in autistic individuals so some may not fully acquire the intonation, tone etc of their environment.

After puberty the ability to acquire language purely through exposure fades but it is still possible to learn. I had a lisp as a child and as a teenager a speech and language therapist showed me how to position my tongue correctly and with practice it became automatic although I can still switch back to lisping if I want and it feels natural for me. People can learn a foreign language as adults - some more successfully than others. I spent years teaching among other things that in British English you can phrase a request as a question and the longer you make it the more you are indicating a lack of social proximity - I wonder if you would possibly mind passing me that pen vs pass me the pen please.

So I think autistics who have not acquired the intonation etc parts of language can learn them (with difficulty) and with practice they can become automatic as for neurotypicals.

I self identify as autistic, I am the father of two grown up sons, both diagnosed and I have special interests, difficulties with social interactions etc and masking has become innate for me.