A bit of late entry to this thread, but very interesting and coincides with some of my experiments exporting terrains via the micro exporter.
Experimented with single thread render to output an .obj via the micro exporter which does reduce duplicated components to some extent, but not entirely. Can see how the more buckets can produce duplicated faces along the "seams" of each bucket and rendering with a bucket size that encompasses the entire dimensions of you render (i.e a bucket size of 1024 for a 1024 square render) might eliminate that. To answer Dorianvan, in my experience larger buckets mean more memory (in other render apps) - usually reducing the bucket size is something to try when running out of memory for a render - never had to tweak it in Terragen, but larger bucket for a render node solely optimised for micro export shouldn't be a problem.
However I feel all this is moot, as the output mesh will always have duplicate vertices and single thread renders and larger bucket sizes won't fix that. So the mesh will always need some cleanup to behave properly in other 3d apps. Find an .obj editor that has a remove duplicate vertices and faces function and run that on your mesh and you should be good to go and of course you can then run multi threaded to speed up your output.
I'm currently working on something that should enable to output of very hi-rez terrains (at least for Maya users) via .obj and vector displacement - not ready for release just yet though. But if a brave soul (and a Terragen/Maya user) might want to try it out, they can PM me.