Totally disagree. I almost never order an entree without some modification. I don't do that to be a jerk but I'm not going to let anybody else decide what kind of side dishes should go with my porterhouse or my roast chicken. SO instead of say mashed potato and corn, I might elect to have two sides of broccoli or a side of broccoli and a side of butternut squash. In over 20 years of going to restaurants on a regular basis, I almost never have a problem getting the sides I prefer. And if I want my steak with or without mushrooms and onions on top, I should be able to decide that as well.
Now in a fast food joint like McDonalds or Taco Bell where speed is key, I can see where that kind of accommodation would gum up the works. But in a sit-down restaurant where you are going to be paying upwards of $25 per person, you ought to be able to expect a higher level of service and get the food the way you want it. (That's why you tip in sit-down restaurants but not at McDonalds and Taco Bell.)
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.