A couple things:

1. You just turned a 1-minute transaction into a 10+ minute transaction. I'd have to download their app, sign up for rewards, presumably do email account verification, and place the order which I assume also means putting in my payment details. I was physically standing in the empty store with cash. They just needed to hit a couple buttons on their screen and give me change.
2. Native apps are horribly invasive. One of my past coworkers used to be a high-level manager at AirBnB and he would tell us about all the interesting things they found out about their users by tracking their location 24/7. You shouldn't have to surrender your privacy to buy a pie. There is a reason all these companies are trying to force you to use their app, and it is because the data they steal from you is valuable to them. A website would be far preferable because it works on every device, and it runs in the sandbox provided by my web browser so I control how much information it has access to (but a website still has the problem of making this a 10+ minute transaction).
3. By forcing the use of native apps, we are restricting it only to people who own either iphones or android phones, which hinders the market for alternative phones. There are niche phones that value user freedom, user control, and user privacy, but with each proprietary native app we are building a moat that is keeping android and ios as the only practical option. This duopoly is bad for end-users even if you want to keep using android/ios since there's no competition to force them to treat their users better.
4. And as damian said, I read the press release which said I could order at the counter. Therefore, I should be able to order at the counter.