Yep. You'd need to import the model that had each level assigned to its own shader. I'd set out the wind system in the main network view and assign the wind shaders manually: Global wind everywhere, trunk wind masked by global, branch wind masked by trunk, leaves wind masked by branch. One shader-tree of wind nodes assigned to each object manually. I've done lots of wind experimentr with Terragen, from single objects to multiple part objects, I really think that the most convincing style to use would be an internal, procedural method. You don't have any chance of a repeat pattern forming and, although apparently random, TG's procedurals are so open-ended that they are really not that hard to tame at all with a built-in black to white gradient system. Of course, though as always, there's multiple ways to skin a Terragen cat but I think the procedural method is really much less work and playing around than external model editing, and such. Many other applications have this functionality built-in, of course you know that, but I know Terragen does, too, it's just not a selectable 'feature' yet. A little messing around to contain it into a few internal nodes is probably the option I'd prefer.
I'm really interested in seeing your ideas, too, though, don't get me wrong. I'd just rather create an inbuilt system that was easily globally controlled with internal nodes, than need to mess around in another application, which would be tuned to a particular scene. Know what I mean? Like I said, though, many ways to skin a digital cat, and all have their own ups and downs.