Well finally I have the car back 3 weeks to the day since it went in. I'm going to give Donny VW credit cos all the rattles and creaks are gone and the car is now back to its brilliant best. Still love it.
The alarm issue, however, has proven an unsolved mystery in that it will still only engage if you do a lock, unlock, lock routine i.e. the second time you engage it, not the first time. They have changed door control units, inclination sensors (the fault code Darren spotted they did eventually see on their system), checked voltages and God knows what else so I can't fault them for trying. They've also been constantly in touch throughout which also helps as many dealers just don't bother.
Anyway, VW have now told them to strip parts off another GTi and swap them onto mine. Fair enough I suppose but Donny don't have any GTis to swap with so I said I could quite easily live with it until they find a donor car.
Now, I suppose one could argue that VW is effectively admitting they don't know how to fix it. However, I'm feeling magnanimous since I've got my pride and joy back so will let them off. The dealer showed me the file of reports, emails and technical directives that now belongs to my car and it looks like War and Peace but at least I know there have been efforts to sort it.
So, well done Donny for fixing all the other issues. I now have a car that feels like new again. Shame about the alarm but I'll survive with it for the time being and Donny will continue to get my custom.