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According to the EnergyPlus Engineering Reference Manual section 4.2, a simplified model is used instead of a finite difference model. In this simplified model there are 2 nodes for the heat transfer model: one node at the surface of the soil and the other in the foliage. The moisture balance also uses 2 nodes: one at the surface of the soil and one representing the average soil moisture through the entire soil depth.
Note also that comments in the source code suggest that only 1 ecoroof construction can be employed in a given model. I am not sure if this is still limitation.
Hope this helps!