McDonald's did indeed help Chipotle get their logistical systems in order. CMG and MCD still share some common suppliers.

One area where Chipotle resisted McD's advice was in automating their kitchen systems. One example was the steak. CMG believed hand-marinating and grilling their steaks in-store was a core feature that couldn't be changed. It's also a highly risky procedure when it comes to food safety and cross-contamination.

Other things, like the carnitas and barbacoa, were changed to be prepared offsite and shipped to the stores for sous-vide rethermalizing and serving. The steak was also changed to this method after the outbreaks (and long after MCD divested).