***Neither a teacher nor a native speaker.***
I can only guess:
Probably it is possible but in your example it makes no sense to me.
I wonder where the rainbow does begin.
In my opinion the emphasized word (in spoken English) would be where.
Where does the rainbow begin?
So maybe the main sentence should be:
Does the rainbow begin?
I wonder if the rainbow does begin.
(However, in that sentence if could be emphasized too.)
Anyway it's only a guess and I'm very interested in reading the natives' opinions.
Student or Learner