I’ve found Panera Bread’s online ordering system to also be a well crafted order flow. To your question, I wonder if the exact reason they don’t is because they view their order software as something that gives them a competitive edge in their specific cuisines markets.

Panera and Chipotle are about as far apart as you can get, sandwiches and soups versus burritos and burrito bowls yet where I see some alignment is how they both have amazing online ordering experiences which allow deep order customization that eschews a lot of friction in doing so. I can’t think of another large chain with similar order experience between the two (Edit: Potbelly, perhaps for sandwiches?)