AFAIK, Wal-Mart is the only retail store that negotiates directly with Visa and MasterCard, and that only really happened after it sued both card networks a decade ago over being forced to accept cards with higher fees if it wanted to accept debit in its stores. They're still not happy with what they're paying; they urged a rejection of the settlement offer in the latest class action suits over processing fees because it still left Visa/MC's ability to raise those fees when they want intact.

So it's likely even large chains like McDonalds still pay the 1-2% interchange rates everyone else pays, just with a lower markup than average. They do pre-negotiate rates on behalf of their franchisees, which own the merchant accounts for their individual stores.