I think there are differences, though we had not sorted out how to adequately distinguish them. I think in the interest of science the psychologists' ADOS become a gold standard and what they observed in the present became what determines diagnosis. And, in a few short years, every child diagnosed with autism who learns to talk has come to be rediagnosed with Aspergers, in complete contradiction to the definition, which was then changed by DSM 5 to fit the need to pidgeonhole, since high functioning autism is, just my opinion, too hard to distinguish solely by observation using one structured test, from Aspergers.
I also think there have to be brain differences in people who struggle to communicate more, as may relate to the now defunct autism/Aspergers divide. If nothing else, our brains are plastic and speaking and understanding less and/or differently, like reading more or less, or hearing, or seeing, has an impact above and beyond whatever differences, if any, may exist at birth.
Whether the differences are fundamental, or cosmetic, that I have no idea. But I have no doubt that years of practice talking very young versus years of struggle without much practice until older impact our brains, and who we are, and how we experience the world, and ourselves, and our lives. And how others experience us, as well. Even if we start out the same.