The factor of safety limit equilibrium equations are derived in terms of total forces, so the program uses the rock unit weight you define in the Input Data dialog to determine the wedge weight.
You would enter the saturated unit weight if the wedge was below the water table, although in rock there is usually very little difference between the dry and saturated unit weights. Effective stresses are computed on the joint planes for use in strength calculations by subtracting the pore pressure from the total normal stress. The effective stresses are not computed by first computing a buoyant unit weight and using this, although you could formulate the limit-equilibrium equations this way and get an identical result.
To summarize, the program properly accounts for the fact that the wedge is below the water water table.