The incidence uncorrected sigma nought is, if I understand your question correctly, beta0. The relationship between sigma0 and beta0 is: sigma0 = beta0 * sin(inc angle) and so beta0 does not include the incidence angle correction. The calculation of beta0 is given in Section 4 for the document you mention, i.e. beta0 = DN^2/Abeta^2 where DN is the product pixel amplitude values and Abeta is one of the calibration LUT’s in the product annotation.
Note that if you want the beta0 of a distributed region (rather than a single pixel), it is important to calculate the average pixel intensity of your region (average DN^2) rather than the square of the average pixel amplitude.