I don't know if the concerns are misaligned, just the reason for the concern. The app creators specifically said they created it to reduce food waste, but I think the app creators have put too much stock in the benevolence of restaurant owners. If they are selling food that was not leftover, it kinda defeats the purpose. Ultimately is it a horrible thing? Probably not since it doesn't move the needle in the other direction, but it is misleading.

The one thing I can see making things worse is the last thing you mentioned. If they were going to donate the food to a local food bank, then ultimately the app makes the world worse and doesn't do the thing they set out to do. Kinda like Imperfect Produce, Too Good to Go could be a net negative.

Anecdotally I took a look at the places around me just to see. I live in a pretty low participation area (not a small city, I'm in the Seattle area), so grain of salt there. Of the 4 restaurants within 5 miles of me on the app, 2 were donuts, which seems like a good use. I took a look at reviews of the 2 non-bakery restaurants, and one seemed like it was using it as intended. The other was called out in reviews, with multiple people saying the employees explicitly told them they were instructed to put specific low cost items in the bag.

Overall I think there is something to look into, but the article just hits it tangentially.