The place I usually go to on the weekends has a menu that is 2 pages. They have maybe 30 items on there including the appetizers. 1/3 of the items are fish, which I don't like. If I couldn't order burgers without the tomatoes and pickles I'd be fucked. I guess I can pick them off but why not just ask for them not to be included so they're not wasted? I can see your point if they're making things in big batches and can't reasonably leave an ingredient out but for shit like sandwiches/salads/pizza or whatever it's not a big deal to leave something off. It's certainly not an insult to the chef to not like an ingredient. Taste is completely subjective, if you're insulted by someone having different tastes than you that's a you problem.

There are a lot of mushroom or chicken dishes which will also have bacon or sausage. For people that don't or can't have red meat, they have to ask that that be kept out.

Sometimes it's the easiest way to get a particular toppings group. Like a "mushroom burger" comes with Swiss, bacon, sautéed onions, and some sauce, or you can build your own for 10% more than getting a pre-built mushroom burger, minus the mushrooms. Plus, when you and-then an order, there's a high chance they'll miss something.

I mean, my local place asks me every time if I want to add peanut butter to my burger. I'd also expect modification to be more and more frequent with the prevalence of touchescreens allowing customers to highly customize items. I don't see modifying as a big deal, within reason. Not just for burgers, obviously.