Hi everyone-- My two cents, as I haven't seen this mentioned.
The most common allergens besides dairy and eggs are wheat, corn, and soy. The MOG obviously isn't allergic to flour, so it's poosible she is allergic to the soy or cornoil in the box mix (as my stepdaughter is). You should NOT have to make a scratch cake for one person who isn't going to be paying for this cake anyway! Let her eat chocolate! Otherwise, I agree with Melvira:
1. Ask what the specific allergy is (for "legal" reasons)
2. Do what is best and easiest for you
3. If you go through the additional expense and time of making a cake completely from scratch, politely let them know that the "accomodations" will result in an unavoidable increase in the price of the wedding cake.