Multitronic fitted to a 2.0 or non quattro 2.7 are reliable if the gearbox has had oil/filter change every 40k miles without a gap. My view is there's more of them about so more threads with faults on them? I rarely seen threads or posts of people stating wow it's been x mileage/ownership time and my car runs perfect.
The later multitronics (07+ cars) have the improved internals I think from reading stuff on web.
But if you compare the driver experience of a multitronic vs a tiptronic you probably wouldn't want the multi and happier with the tip.
Perhaps look for a 2.7 quattro auto as that will be tiptronic but then a 3.0 is probably better? The 2.7 is derived from the 3.0 and share most parts.