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Heat transfer through transparent surfaces in EnergyPlus is calculated using a steady-state heat balance across each pane in the construction. Your choice of Conduction Finite Difference (CFD) or Conduction Transfer Functions (CTF) will not impact the transparent surfaces.
For the ground below the greenhouse, I'd recommend using the Foundation boundary condition with a slab and footing that have the same materials as the soil. This boundary condition will calculate the multi-dimensional heat transfer through the ground using a finite difference calculation.