I think the trick here is that Doordash isn't charging the customer $x + $y, but $x - $y. X minus Y. That is, they're subsidizing the delivery - in order to generate demand, and then come to the restaurant with the data to convince them to sign up for 1). This was actually mentioned at the bottom of the article.

So in this story, 'JumpCrisscross paid $x-$y = 5k for an order to a homeless shelter, but the real, restaurant price for that order $x=20k, which means DoorDash has just subsidized the transaction for $y=15k. The restaurant got an extra $20k of business that day, and 'JumpCrisscross bought $20k worth of food for a shelter at 1/4 the price.

And the best part, they could probably do it again :).

EDIT: Reading the article again, it seems to me Doordash is supposed to be charging the customer $x in the lead generation phase; so perhaps the -$y part is a scrapper error.

Or the -$y is marketing costs.

DD says to Pasta House, see? Look, with DD we facilitated an additional $20k of revenue for you on this day. You should enter into an agreement with us so that we can make this a more seamless process.

In most cases, Pasta House isn’t aware that those orders were drastically under cost and don’t represent actual demand.

It is exactly the opposite of your #2, check out the article.