The web version of PVWatts doesn’t take into account the effect of one row of panels/trackers casting a shadow on another, and neither does it account for backtracking in the morning and evening to avoid shading. Essentially, you are modeling the performance of a single tracker.
NREL has a page devoted to derate factors here which provides a rough approximation for a shading derate based on GCR (ground coverage ratio), but in reality the affect of backtracking is dependent on location.
With this in mind, I modified the PVWatts source to calculate the correct incident angle (function incident2) for a horizontal single axis tracker given a GCR, and ran the simulation for a number of GCR’s and locations. Here is a sample result:
This shows the actual derate factor you can expect as a function of GCR for 3 different locations. Clearly, they are NOT all the same! At a GCR of 40%, there’s a 1.4% difference in energy lost between San Diego and Salt Lake City.
With small changes like this I’m getting closer to a model that accurately predicts real world performance.