a warm welcome to you! I hope, you will find this forum helpful and supportive!
You are right, there seems to be a contradiction, as vitamin D3 indeed strengthens the immune system and helps to fight off common colds and the like. In my lay understanding, I imagine my immune system as simply erring, and erring from weakness, so that supporting it (by supplementing vitamin D) will not make it more aggressive and more dangerous to myself, but less erring. This, of course, is no scientific explanation, why vitamin D3 helps and how. I do not even know, whether anyone can explain this sufficiently (I would have to search the OMS book, to see, whether it is being explained by George Jelinek. But, perhaps, others in this forum know the answer without having to look it up?)
What I remember clearly from the book, however, is, that there is ample scientific evidence (many studies! See the references on “step 2” in the book!) that a) high vitamin-D levels have a preventive effect against MS and b) even after MS diagnosis reduce relapse rate and improve clinical outcome. Therefore, there is sufficient evidence that vitamin D3 is beneficial for us — even, if there might not be an absolutely satisfactory explanation as to why this is case.
Hope, this helps, even if I can’t answer your question!