Why would there be coffee spilled on the thrust levers of an automated airplane? There is not a robot in there drinking coffee, and presumably they don't just put the thrust levers in the cabin with the coffee drinking passengers. You don't have people in the wheel wells either debugging issues, you rely on the systems to work.
AI can definitely talk to ATC, in fact it could disrupt ATC who could send declarative commands to planes to remove chance of miscommunication.
Even my Telsa makes decisions about changing weather conditions (eg. disables automated lane changes in heavy rain & such, AI controls the wipers)