I was messing around with the Disneyland app this morning and was surprised to see there's really no option for customization there, either. I've used mobile ordering there dozens of times and if you had asked me, I would have (incorrectly!) told you that you can customize your orders.
I understand why they might prefer to limit customization (it has basically singlehandedly ruined being a Starbucks barista!) but at these quick service locations where things are assembled on a line and aren't typically pre-mixed, the orders (with customizations) should just print up on an order ticket. Anyway, I guess we'll see how this develops but if I can customize my Taco Bell order to absurd proportions, we should be able to make modest changes to our theme park food orders.