I want to dump on Newegg here, but selling on Ebay is a nightmare these days. There are so many scams, bogus messages, demands to change shipping address (never do this), bots, and other BS on that platform. I think Newegg should be providing more money when you trade-in during the purchase of a new product. At least they're not being GameStop levels of evil here.
Yep, the article seemed to miss this point. If one were selling the card on eBay, they risk the possibility of someone getting the card, claiming it doesn't work, and returning another defective card in its place for a refund. Or simply breaking it due to user error and requesting a refund. Then, eBay sides with the buyer, and you will be stuck with a defective card worth hardly anything, and not much to do about it. There is almost certainly less risk involved when trading it in to Newegg, even if the potential return is lower. Newegg needs to account for things like that possibly cutting into their profits when they resell the card. They also need to pay for testing and refurbishing these cards. There could potentially be some intermittent problem with the hardware that doesn't get caught by testing as well, but that gets reported by the eventual buyer. Plus they have to deal with shipping costs, both for the person buying the card, as well as for the one trading it in.
And looking at "sold" listings on eBay, a number of 3090 Tis have been going for well under $800, so the article's suggested "average" price of $881 might be a bit generous. Unless someone has already done a lot of selling on eBay with a lot of positive feedback, they might potentially struggle to find a buyer willing to pay anything that's not well below average. Some of these sold listings may only bring in around $650 to the seller after fees are accounted for.
The markup is likely not really all that that different from something like trading in a car in at a dealership. And I suspect a lot of people probably don't want to mess with selling a graphics card on their own, and would be plenty willing to make maybe 25% less from the sale of their card just for the convenience of having someone else deal with it. And in the case of the 3090 Ti, if someone is already trading in one of those, they might not care all that much about losing a bit of money off the sale. We're talking about a card that launched for around $2000 just a year and a half ago, that has already lost over half its value on the used market.