I'm not sure of the brands, but i know that the mac and cheese at Cafe Orleans is delicious and not bright orange! I'm pretty sure it's more of a home-made type of sauce and is natural yellow cheese color, tasting like a real cheese instead of the orange powdered cheese on many of the other kids mac and cheeses around.
have you talked to Disney Dining to ask? When you go to any dining place you can ask to talk to the chef about allergies, and the dining cast member told me that they can come up with a dish that meets allergy requirements. I just talked to them about my LO's egg, nut, and seed allergy and while they noted it in our PS reservations, they said it works the same with all counter service as well.