I'd mentioned asking the nutritionist about it because in our case, we just added this to our daughter's regimen, and also just adjusted her enzymes. Regarding both, I spoke to the dr but then he told me 'when J(dietitian) comes in after we confer, she'll talk to you more about how she's been eating and discuss what we decide our recommendations are for handling this.'
So in Emily's case, she would have been completely knowledgeable about the course of action recommended for her and why. She couldn't change what had been prescribed if I approached her later, but she could explain the reasoning behind it, discuss it knowledgeably, if needed talk to the dr and get back to me. I'm also comfortable discussing this stuff with her due to her extensive familiarity with Emily's diet, etc- we get into far more detail about that than I do with her dr (that is what she's there for, after all.)
I do agree that if you do not agree with a course of action prescribed for your child the dr needs to know about it since only they can change it- but feel there is value including the dietitian in the discussion if she is knowledgeable/you trust her or was involved in the decision to put your child on it in the first place.