I think that reaction stems more from the comment outright seeking to create a hostile atmosphere about it, not from being clear on preferences in itself.
It's the same thing with customers who make a big scene about a missing fries or something. 99% of the time it's not a problem and nobody cares - here's your fries, have a nice day. 1% of the time the person cares less about the fries and more about being hostile about it on principle/for fun/for respect/because they are in a bad mood/whatever, and those are the ones that suck to deal with when you're there but not in charge.
Indeed. I think anything short of tossing your drink at McDonalds workers probably doesn't phase them. They deal with much worse shit from the public than somebody snarking at the premise of having an app.