That's OK as long as the restaurant normally has those sides on the menu. But when a customer says I would like the sausage and peppers without the peppers, Phili Cheese Steak without the cheese, etc, then there is a real problem.
I can see your point there. I would never ask a restaurant to actually alter a menu item (such as removing beans from a bowl of chili). I usually limit my “special requests” to side dish substitutions.