This whole affair and others like it, baffle me.
From my limited experience with ATC (maintaining nav aids & comms in Saudi), I remember flight plans preceded a flight so the relevant FIR would be aware of what was coming, from where etc with approximate times planned for various reporting points. So there should be no surprises when aircraft appear. I agree it is bloody awkward when there is no communication with the aircraft. I once watched a Syrian Airlines flight from Damascus to Jeddah being forced to land at Tabuk as it was 1 minute late reporting entering Saudi airspace!
Meanwhile, London reported no comms with the aircraft on 121.5MHz, yet the RAF called him on that frequency. Nevertheless, once the Typhoons had caught up with him, presuming they established comms on that frequency, could they not then instruct the pilot to contact London on the correct frequency?
Finally, this business of threatening to shoot down aircraft that could be construed as posing a threat to urban area etc; the UK is not a vast area. So, imagine shooting down an aircraft approaching London after deciding it posed a threat to the city? "Oops! He has crashed in docklands". Job done as far as the terrorist is concerned. During the Olympics, the government posted anti-aircraft batteries near to the Olympic venues so they could shoot down aircraft posing a 9/11 type of threat. And where would they come down? Blow it up over Dartford and watch a couple of 5 ton engine lumps flying in a ballistic arc toward London anyway? (Shades of the Buccaneer!)