I tend to go with the opposite - take something off that normally comes with the food or ask for an alternate topping. Pick something like cheese or sauce so they can't just scrape it without it being noticeable. They'll make it special just so it doesn't look bad.

On the other hand, if you are asking them to remove something that you are allergic to make certain that you tell them that it is for allergies. My sister spent the evening of her most recent wedding anniversary in the emergency room because the restaurant thought that scraping the avacado off her food would work when they didn't make it right the first time!