When you preorder there are options to leave off items such as the sauce but I do not remember any options for substitutions-not sure if you order in the restaurant if it is any different as we always preorder.
My understanding (haven't been yet but have seen this subject come up) is that you can ask for certain items to be left off (so no tomatoes or sauce would be available), but substituting items such as sauces will not be an option. Ordering at the restaurant vs. preordering should make no difference; either way you input the selections yourself from what's available on computer/app/on-site kiosk. @TheRustyScupper frequently posts that BOG is Disney's test case for how people handle not being able to make any substitutions.
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