At CS locations, my recollection is that if the whole meal is a premade specialty mean (pizza, chicken tenders, mac & cheese, etc) then expect to pay approximately $2 more for your meal but if you're just getting a gluten free bun or having BBQ sauce left off and the rest of the meal is a "regular" meals (prepared with allergy precautions obviously) then you pay the same as everybody else. Desserts are similar price to the regular ones but they're typically smaller. If you'd normally be ordering a kids' pizza then I do believe you'll be paying for an adult allergy one rather than a kids' meal unfortunately (I think; we can't actually eat the pizzas so this is just what I think I've read).
At TS locations, I've never paid any kind of premium for safe foods though I have read of at least one person on this board who was charged something like a $2 or $3 fee.