I think the percentage threat is less about what data some bad state actor can collect and is more about that fresh Insta pic with some classified screen up in the background.
Should the tube be treated like a SCIF? Maybe...I've never been in one so I don't know. If it does, then it should be treated like any other SCIF, leave your phone outside in a box by the door. Banning phones from the plane, or making people put them in Faraday bags is just draconian policy from people just looking to cover their own ass.
AF One has an entire press room. I'm sure the technology exists to both protect classified information and use common electronic devices for reasonable work.
As far as the physics app goes, who gives a shit? It's a 737 on an international flight plan, even in "combat".