How does PondPack calculate flow for an unsubmerged circular orifice?
First, it calculates critical depth for the circular shape. If the tailwater for the orifice is less than or equal to the calculated critical depth then the velocity head is added to critical depth to compute the upstream headwater elevation. However, if the tailwater elevation exceeds the critical depth, it performs a standard step backwater calculation for a thin culvert to compute the headwater elevation. According to the developers, inlet control calculations do not enter into it.
This workflow is used because it tends to be more realistic than a straight linear interpolation, and also allows for a smooth transition between unsubmerged and submerged calculations. The reason the area orifice does not do this is that we do not make any assumptions as to what the shape of the area orifice is. Because the shape is not accounted for, we do a simple interpolation.