At face value non-partnered restaurants dont lose money, they simply get more customers (essentially, getting some of the services that partnered restaurants get, but for free since partnered restaurants pay fees for each order that goes through the platform)
However, in truth they pay damage in reputation. If the delivery company delivers food slow, or lets it get cold, then the customer will blame the restaurant. On top of that, unpartnered restaurants will naturally get slower delivery times because the order flow involves grubhub delivery people walking in and placing an order (or calling in), whereas partnered restaurants get point of sale systems integrated with grubhub's backend. They get less accurate delivery time estimations. They might pay a much higher delivery fee or service fee. All things add up to a worse customer experience.
While I agree, restaurants do tend to pick up on this over time because (more issues with Place & Pay) people will complain to the restaurant about food being cold/slow not realizing that the restaurant isn't even involved in the delivery. Sometimes the delivery people make it quite obvious (e.g. drivers are given GH branded credit cards to pay with)
[ Disclaimer: GH employee but speaking independently & not representing the company in this message ]
You're mixing up controversies - there was a separate "feature" Grubhub did years ago where grubhub would stand up online presence for restaurants to bring in web search traffic (branded websites, search results on grubhub.com, etc) and list a grubhub phone number instead of the real phone number so that grubhub could collect comission on the orderflow that they're raking in for the restaurants. These were partnered restaurants, so they were signing up for this and could opt out of any of these services, in theory anyways I wasn't part of this so I have no idea if it's really that easy to opt out
Separately, a practice pioneered by ubereats and doordash, "Place and Pay" is a new thing in the past 2-3 years where Grubhub will just list a bunch of restaurants without them asking for it ("non-partnered"), and when you place an order online the driver will go in and order takeout, then carry it to you. The restaurant can opt out of this, but they never asked for the service in the first place so it's kinda shitty. That's what this article is about.
Grubhub was against place and pay at first, when UberEats and Doordash began doing it (not because Grubhub is selfless but because partnered restaurants are way more profitable), but resisting place and pay turned out to be a recipe for losing market share so that's no longer the case.
However, in truth they pay damage in reputation. If the delivery company delivers food slow, or lets it get cold, then the customer will blame the restaurant. On top of that, unpartnered restaurants will naturally get slower delivery times because the order flow involves grubhub delivery people walking in and placing an order (or calling in), whereas partnered restaurants get point of sale systems integrated with grubhub's backend. They get less accurate delivery time estimations. They might pay a much higher delivery fee or service fee. All things add up to a worse customer experience.