How much better is a 4" / 10cm offset from the roof, versus a 2" / 5cm offset in the racking?
The Sandia temperature model (the default in HelioScope) uses different coefficients for whether a module is fixed-tilt ("open back") and flush mount ("closed back"). So it's reasonable to ask about the implications of adjusting the air gap on a residential system - after all, a wider gap should get more air flow and therefore run cooler on hot days.
Unfortunately, the Sandia model does not provide documentation on the specific gap distance used for the "closed back" measurements. Nor do they provide guidance on the variable impact of changes to that gap distance. So ultimately, it's up to the user to make adjustments to the coefficients in the temperature model (which can be done in the Condition Set).
Advanced Option: Manually Editing Coefficients based on System Advisor Model
There is a temperature model that does relate module temperature to the air gap from the roof: NREL's System Advisor Model includes a CEC temperature model with air gap as an input. While this is not directly incorporated in HelioScope, it can be used to estimate the relationship between module height and temperature losses.
We did some initial analysis, and we found that Sandia's temperature model matches CEC at 2cm (0.75 inches), while for an 8cm (3 inch) height, one should adjust the temperature coefficients to A = -3.22, B = -0.0655.