in order to make him sit you might have to make it more interesting to sit so let him try to grab something which is out of reach so he has to flex. Apparently the extension reflex is far to big so you have to stay away from extension. Any support= stimulation of the back will increase extension. in order to control that he should always sit in a position of more than 90 dgrs hip/ knee flexion (ideal but not practical).
Another possibility is working in kneeling position because you have to prevent stimulation of the back! (it will increase extension). Or for sure crawling position. I expect ataxia as well so the more support the better but avoid stimulation of extension. Prognosis is poor unfortunately but what you can mean for him extremely important. Wheelchair bound is likely his future and this should be your first goal, transfers always in flexion, use a turn safe which will break extension and help with independence.