All he would tell us was that he didn't need surgery for it
That's great news! It is always better to avoid surgery if you can.
but I just wanted to know why my son's endurance and fatigue issues never improved and why he developed scoliosis when no one else in the family had it.
Everything I've read suggests that most scoliosis is idopathic. So most people will not have other people in the family with scoliosis.
Hypotonia is a risk factor for scoliosis. That's part of why kids with hypotonia would typically get strengthening exercises through PT and will be screened for scoliosis more often.
And, again fatigue and lack of endurance go with hypotonia. I don't think a neurosurgeon is at all the right specialist to see to better understand hypotonia. It isn't what they do.
All of these tests are causing so much anxiety and taking up so much of our time but we have to rule out a few more scary things before we can stop.
What sorts of tests are so time consuming? The MRI should not take more than a morning or afternoon max.
I went online to see what they might be wanting to rule out and read about some really scary things that could require risky surgery on his spine.
I strongly urge you not to Google. It isn't going to help. They are doing test because it is required to rule stuff out. As I posted before your chance of getting a firm diagnosis to explain nonprogressive hypotonia in a twelve year old is very low. I think your best bet would be to focus on the ways he's made progress and will continue to do so. There are a lot of kids who never get a diagnosis and that includes not just mildly affected kids like your son but many who have really significant and scary stuff going on.