I just checked .. and Dr. Atkins does discuss Food Intolerances in New Diet Revolution, chapter 14 in the 1999 edition (blue cover). I'm sure it's also covered in his newest edition, as it's a serious issue with weight control and diet-related illness.

Actually, here's the search results page for "food intolerance" from the Atkins official website, atkinscenter.com.

Hope there's something helpful for you

Doreen