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As you say, let's use fluxes (nJy) instead of magnitudes. In addition, we need flux uncertainties. (the uncertainties are covered in DAMD-84). These fluxes should not be corrected for the Galactic extinction. We will 'apply' the Galactic extinction in the flux calibration (we infer the intrinsic spectral shape of a specphot std from the stellar typing using photometry and absorption lines, and then apply the Galactic extinction to it to make the 'expected' spectrum that we observe). I wonder if it would be useful to have a fiducial E(B-V) in pfsDesign...? There is a few Galactic extinction maps in the market and I do not know which one is most popular these days.
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