Quite a big "if". I don't know of any reason to believe it was anything other than one insane pilot. One of the other things your "operation" has to do is plant the flight plan on the pilot's PC.
That is indeed another improvable alternate theory.
From my perspective, it's unusual to commit suicide in such a silent way, with such elaborate attention to detail. He could have killed the copilot, and had knowledge about disabling beacons, perhaps also about avoiding radar detection. But why? As an elaborate prank in creating the greatest mystery in aviation history?
Hijackings are usually far more loud. Distress calls, passengers contacting loved ones, a manifesto is published, or the airplane is destroyed defiantly (GermanWings, Q400 2018 incident, ...).
Given that any explanation must be extremely unusual, I think the explanation that only requires one weirdly competent and motivated person still has an Occam's edge over one that requires hundreds of such people.
Quite a big "if". I don't know of any reason to believe it was anything other than one insane pilot. One of the other things your "operation" has to do is plant the flight plan on the pilot's PC.