I have made this as a raincoat, without the insulation, and left off the pockets. I have also made a lined wool coat with welt pockets from a different pattern, so combining what I recall from those two experiences, I’m going to say that you should be fine making it with the Thinsulate attached to the lining, and putting in the welt pocket when you construct the outer front panel. How important is it to have the extra warmth in the pocket area? The body of the coat would keep the child’s body warm, and that would communicate heat to one half of the pocket (let’s call it the palm side). So with hands in pockets, the only part that had wool but no Thinsulate would be the backs of the hands. You could add Thinsulate to that half of the pocket bag without too much trouble, I think (I recall it being quite thin indeed when I saw it in the store) but it might not be necessary.
Hope this helps!