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The NDVI product is computed from Rayleigh corrected reflectance. Over land, l2gen computes the Rayleigh contribution following the work of Jacques Descloitres (briefly described in Gumley, Descloitres, and Schmaltz. 2003. "Creating reprojected true color MODIS images: A tutorial." University of Wisconsin–Madison).
Any reasonable Rayleigh approximation would do to create the "surface reflectance" values (in this sense 'surface' is land+aerosol).