Very interesting. My understanding is that chairi is frequently misdiagnosed as other conditions. It is really frustrating that it took until age 12 before he got an MRI. It is very typically done in the early years for kids with hypotonia. I hope he's not still seeing the same pediatrician who did such a poor job getting appropriate testing and therapy.
Did they seem at all surprised that while he's technically not got chairi that he would be having such severe symptoms? It seems rather odd that they'd say the headaches may not be related but the hypotonia and SPD would be since headaches are the most classic chairi symptom.
If he's not a candidate for surgery, what do you think you've gained with the diagnosis. What will change for him? Are there areas with less frequent or significant changes in barometric pressure? (I get migraines with barometric pressure shifts as well and I know they are not uncommon for people without chairi).