So I always assumed they were a paying sponsor. Is that not the case? Either way the tribute from Arby's is done to "Thank You for Being a Friend," better known from The Golden Girls, and features some of his jabs at the company from over the years.
The official Arby's Twitter account even posted a mock-barfing Stewart animated gif and the tweet, "Sometimes Jon's jokes about us were hard to digest, but we kept watching anyway. ". (https://twitter.com/Arbys/status/629127518310678528)