If this is really a fabricated false flag operation the internet would be humming with red herring posters to keep the docile minds looking in other directions.
Two scenarios, its been stolen by Iran to destroy Israel.
Its been stolen by a group with instruction to paint it as a complete Muslim operation but its then directed to strike a US target with the intent of initiating an Executive Action that would declare martial law, suspend elections etc.
I've seen this comment several places. What makes this plane more useful to Iran than all the ones that already are in use by Iran and by their allied countries in the ME?
I think avaiation experts will shoot your theory down pretty hard. Besides, Iran has enough jet of their own that the world is not looking for!