Tdiman is absolutely correct. It is essential that the correct procedures are followed in repairing aluminium cars i.e. a job best done by experts. Make sure you are not fobbed off by your insurance company. If both drivers side doors are damaged it will mean possibly that the B pillar also needs replacing. This part is a special casting and how it is re-joined to the rest of the space frame is crucial regarding future crash performance and the fit and finish of the new doors.
Audi have produced aluminium cars for some years now and repair procedures will be well sorted by now. Yes using the right tools is important, this also applies to lesser steel bodied cars. Contact corrosion, galvanic corrosion is a well known fact and the repair centres will be well aware. I think that the risk here is small, but getting the repair carried out by experts is essential. The paint should stick the same, as usual it is in the preparation where the quality of rapair shows. A2 are not Land Rover Defenders where the older design plays a part in the flaking of paint off the rear door, there is steel/aluminium contact in the structure here despite the best efforts of LR to make improvements. A2 doors are aluminium with the exception of the lock catches.
The original A8, I heard, could only be repaired at MIRA, so if Audi have a centre each in the North and South then this is a (slow) improvement. Then again there is today only the new A8 and Jaguar's XJ that is produced in aluminium, both having a different concept for the body structure, so the demand for accident damage repair is limited (I hope!).
I'm sure that Audi will make a good job of restoring your A2 to pristine condition, hopefully the other party are well insured and you will not be out of pocket.
