Good question. Given the high profile of climate change these days we get asked about this regularly. Such transitions are commonly used to represent shifts over time in species ranges.
At present the architecture of VDDT does not allow for transitions between "models", where each model is used to represent a biophysical setting (BpS). Because Path still uses VDDT as its simulation engine, it, too, is constrained by the limits of VDDT. However we are hoping to begin work on a new simulation engine for Path in the fall of 2011 that would allow use to overcome this limit and make it very easy to represent transitions between Path strata.
That being said there are some users that are already modelling these kind of effects in Path and VDDT. They do this by manually combining all of their biophysical setting models into a single "mega model", which then allows them to create transitions between BpS within the mega model. Combining models in Path is quite a bit simpler than in VDDT thanks to its cut/copy/paste features. However once you create a mega-model, you can’t easily go back to the individual models ever again. And of course the mega-model can become very large and difficult to work with. This is why we are hoping to tackle this question properly in Path in the near future.