I don't recall ever being charged for things like allergy buns. When the whole meal is a premade special allergy meal (ex chicken tenders, pizza, mac & cheese) then yes there is always a higher price. For modifications to regular menu items, usually there is no extra charge but we do have at least one regular poster on this board who was charged an upcharge for the priviledge of having stuff left off her plate (totally not what they're supposed to do, but they did).
Hopefully most places will have the Ener-G buns back as the Udi's contain eggs. It does sound as though they're on their way back in, at least based on what this board is hearing.