I think it's important for any parent to trust their instinct and keep asking for questions if they are not satisfied with the answers they've had.
That said, my ds1 has ASD and would also have been able to do all of the things you list in your second paragraph. He also has hypotonia, although not to the extent of your ds and is hypermobile in several joints.
I knew ds was 'different' from a young age, but didn't think autism for a long time, because like you, I felt there were too many 'non-ASD' things about him. What I've learned as time has gone on is that every child with ASD is different, has different strengths and weaknesses and they can present so wildly different, that sometimes it's hard to accept that two very different children could possibly have the same dx. As Leonie said, in order to have a dx of ASD, they all need to have the triad of impairments. How those impairments are 'weighted' can vary massively from child to child and changes the way each child is affected.
Ds1 has Asperger's and in some ways is extremely high functioning, extremely academic and appears to be sociable, yet he still has the triad of impairments and therefore meets the criteria for an ASD dx.
Have the dx's he has had stated where they think he is on the spectrum? Do you think perhaps that he might be high functioning and his additional, physical issues are complicating the picture?
I think what you are going through is pretty common amongst parents who are told their child has ASD and a lot of us have at different times just wished it would all go away. Even those of us who knew and pushed for dx still feel like we've had a kick to the guts when we are told the final dx. I also think that sometimes autism is a tough dx to hear because we fear it means our children may be hard to reach and connect with. Try to keep hold of the fact that whatever dx he does or doesn't end up with, he will still be your beautiful boy and nothing will ever change who he is to you.
It's good that he has an early dx, as it means he will get support at a much younger age than many children and has the best possible chance of going on to realise his full potential, but he is still so little, nothing is set in stone and there's plenty of time to work it all out. If you feel you need to keep pushing and asking questions then do it, as his Mum you know him better than any professional who will ever cross his path and as we all know, professionals don't know everything.
On the other hand, if you are feeling totally strung out by it all, is there any way you could possibly make some sort of conscious choice to take a break from pushing and thinking about it for a while and just enjoy your ds while he's little to give yourself some space to think and processes it all? I know that wouldn't be easy to do, but you have to take care of yourself in amongst all this and sometimes we all need to get off the treadmill for a while, in order to try and salvage our own sanity.
Either way I am going to send you some very unMNetty ((hugs))