In regards to the security of the football, one of the major elements to is the lack of public knowledge about how it works. Do you seriously think that level of security can be maintained in the civil aircraft fleet?
RE: Pilotless flights would be indeed a single point of failure system, just like malicious access to the cockpit is a single point of failure today. However, implementing an ability to override the controls from the ground in an emergency, without routinely flying the planes solely from the ground would have prevented a 9/11 style attack. Since it won't be in everyday use, it can be made as secure as the famous "football" the president shleps around, that would trigger a nuclear war.
We have an override from the ground now: scramble the jets and shoot it. The same level of security that results in scrambling the jets can be achieved in overriding the pilot with software.
Testing a security system doesn't compromise the security of its implementation because in production the encryption keys are different.