What makes you think that disabling auto start-stop would have any effect on warranty? It is purely a means to improve the gas mileage for EPA ratings, and has nothing to do with other engine functions.
When you modify a vehicle in any way, the only warranty items it affects is parts that are directly related to that modification. For example, running oversize tires might have an impact on drivetrain or suspension parts, but is unlikely to have any warranty impact on your engine, interior, etc. What warranty-related part of the vehicle do you think would “break” due to auto start-stop being disabled?
Bruce