I have passed long days in electromagnetic testing room, and I can say that you will be surprised by what can happens with complex and highly programmable electronics !
I had to work on a navigation system some years back, I didn't have to spend time in the "bubble" but colleagues did. We certainly did have people who were very aware of RF design and cross talk issues as we had a TEMPEST rated room as they had also been working on secure digital comms.
Your "demonstration" prove that a software modification can open up the frequency range.
True, but it is hard as the radio in a phone tends not to be open software. A USRP would be much better but then you need amplification and power. You are inside a metal tube and you need to get inside an antenna on the outside which is designed to go off when it receives a burst from a 50KW radar. The transponder squirts data back using something like 20w or so. It would be hard to overwhelm that from inside the plane. I would agree that if you hold up to a window, you could get some power outside (a phone does work on a plane on the ground up to a certain height, it is just a weak signal).
Inside the plane, RF goes by coax. Data goes by different means, usually twisted pair. Either way, the data wiring goes from the front-end in the cockpit to the avionics bay which is located underneath the cockpit (so no long cable runs). The FMS does not fly the plane (it acts more as a top-level monitoring system), there are other computers that worry about that.
If you have read the publication subject of this article, you will see that aircraft manufacturers have actually not worried at all about vulnerability.
Please remember that planes ship with standard flight control systems only. Cockpits and avionics are selected by airlines based on different options. It would be quite hard to try out every variant. However flight test has a big increase in general RF "crud" in the fuselage as you have multiple high performance logging and telemeter systems with cabling all over the place.
In the end, it seems that if you want to cause chaos, just get an airband radio and claim to be Frankfurt Radar or something.