He sounds normal to me. My nephew has autism and yes he does hand flap but there were plenty of other signs at the time. He stopped babbling and wasn't saying anything, his speech just went backwards. He would go to the playground and just run back and forth along the fenceline staring at it. There were plenty other things too social probs etc and I know different children with autism will show different signs but basically I think if you son is progressing then I wouldn't worry. Children are all developing in different areas at different rates. As long as they are making progress that is the main thing.
My DD is nearly 18 months she says mumma, dadda (not alwasy to right person) doggie, ball, door, shoes, whats that, apple, poo poo, she tries to say bottle and balloon but the often sound like ball too, not all her words are clear but like you said we usually understand what she is saying. She understands alot more than she says, like we can say pick up the pencil and give it to daddy and she will.