There's not a lot of customization on the Be Our Guest pre-order. I just checked on my lunch pre-order, it will let me choose which side I want with the sandwiches (fries or vegetables). The turkey sandwich does have an option to decline arugula and tomato and/or the dijon mayo. You can choose to have salad dressing on the side or tossed. I can't check the breakfast pre-order since my ADRs are both for lunches.
For BOG, at least, you may be able to ask at the restaurant to leave something off. They don't prepare the meal until you check in inside the restaurant.
For mobile orders at other QS places whatever you see in the app is all you can do through the mobile order. There is no CM interaction until you pick up your food. If you need further customization it would have to be ordered in person.