This is not a common problem I am aware of (I have never had my turbo to manifold bolts loosen up... torqued to the factory spec.) So it leads me to wonder if there may be something improperly installed, or missing, from your setup. Are there any support brackets (from exhaust manifold to turbo downpipe) that are supposed to be present but missing in your application? I'm not too familiar with the vanagon TD exhaust setup but maybe someone else can chime in. I can imagine a big, heavy, unsupported exhasut system perhaps overloading the turbo mounting bolts. The exhaust system should probably be supported somehow. I know that on transverse mounted 1.6TD's, VW put a support bracket tieing together the exhaust manifold to the turbo downpipe, which would seem take some vibrational/cyclical load off of those turbo to exhaust manifold bolts.
Are you thread chasing and cleaning the threads and using copper-based anti-seize prior to bolt installation? Crap in the threads could result in less clamping force than clean, anti-seized threads. Copper-based anti-size is the only thing I've found that can stand up to the extreme temps these bolts see - I really doubt any kind of threadlock would work at those temps.
If all else fails, and you have access to safety-wire drilling jig and tool, stainless steel safety wire through the bolt head certainly sound like one way you could keep those bolts from backing out. It just sounds kind of weird that it would be necessary. Hope this helps! Good luck.