My 3-year-old DD also has atypical intonation. To me, it sounds like a person learning a new language. The first few times they say a new word or phrase in a new language, it comes out of their mouth a bit weird (too high, too low, too fast, too slow). As they get used to the new language, the new words and phrases start sounding more natural. I think my DD is getting better with her intonation, but it's hard to tell day-to-day. I would have to go back and listen to a recording from a month ago to tell for sure.
You might try to throw into your language games some varying of intonation, to see if he can discern intonation differences. If he says "me-ow" in a high voice, try answering him in a really low voice, and see what he does. The more he can play with words and phrases, the more they can become his own.
I am not a professional by any means, just a scientist that likes to over-analyze everything 
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Me, self-diagnosed AS; DS, 7, dx Autism; DD, 5, dx Autism; DH, NT bless his heart!
Speak one at a time. Sometimes my brain runs out of RAM.