Hi Thomas,
I don't know exactly what the Z values printed out by the JEOL software represent. (I'm referring to the 28.0 for N Ka and 78.5 for B Ka in BN.) They are much too large to represent the actual atomic number corrections, and so I deduced that they are Z values for the X-ray of interest in the unknown before division by the respective value obtained from the standard using the same model. Without units attached to these quantities, they are difficult to interpret. Since only the ratios relative to the standard are used to calculate concentrations in the unknown, the units typically are not specified. This is bad practice, and it can create nightmares for those of us who want to figure out how the calculations are done. The A values presented are relatively easily identifiable as f(chi), which is dimensionless.
Also, I should point out that the area under phi(rho*z) wouldn't necessarily have to be stated in units of mg/cm^2, but it must carry units of mass per area (so it could be μg/km^2 or g/cm^2, for instance). I was a little sloppy in my original statement. Note that phi(rho*z) itself is dimensionless.
If you are interested in exploring how the Z and A factors are calculated realistically and precisely (and with identifiable units), then I suggest that you read through the presentation by Pouchou and Pichoir in "Electron Probe Quantitation" (aka "the green book") -- I've attached their paper; the basics are covered in pages 31-45. Note: it is not easy reading! Also, note that typos are present in equations 13 and 21. If you want, I can send you some Fortran code that I wrote based on this presentation.