Example. Suppose you're sitting in The Spotted Pig in NYC. Now, suppose you're not a fan of the Roquefort cheese their burgers come with. You can have your burger at The Spotted Pig with Roquefort or without Roquefort but don't even ask for a different cheese. A couple more examples of the customer not always being right:
*Murray's Bagels (A Johnny fave) in the West Village and Soho will not ever toast your bagel. Never. You can get it a million ways but never toasted.
*At French restaurant Le Relais de Venise L’Entrecôte, don't bother asking for medium-rare meat. It doesn't exist in France and therefore you can't get it here.
Have a gander at the article, from places that don't allow ketchup to others that don't put salt and pepper on the tables, it's a fine walk inside certain kitchen across Manhattan that long ago stopped worrying about your special dietary inclinations.