INO and CFA, as much as I disagree with their politics also don’t franchise, have tight control of their supply chains(In-N-Out grinds their own meat in Buena Park and Stockton, CA), all their stores are company owned and the families that founded them(Synder & Truett families) are still calling the shots at their headquarters, not disgruntled franchisees. And they actually treat their workers decent for fast food(INO pays above minimum wage in CA, CFA is closed on Sundays) as well.
McDonald’s and Starbucks comes close for standards and cleanliness, but the former is franchised. Jack in the Box had to take food safety seriously after the 1993 E. Coli outbreak they had that almost did them in. I hear more E. Coli and salmonella incidents with Safeway’s central meat processing plant in Tracy, CA than I do most fast food joints.