Rfactor is used in any case where two sets of structure factors are compared and scaling is required. This is in contrast to Fourier which is used whenever a single set of structure factors are used or two sets are used without scaling. If you want to calculate difference maps of various sorts this is the place to go.
In addition, Rfactor performs very complicated calculations in its computation of the function value, first, and second derivatives of the crystallographic restraining function. Rfactor has several commands which allow you to directly access portions of these calculations and subvert them to your will. The AGARWAL command allows you to supply special Fourier coefficients to calculate a gradient. The NORMAL_MATRIX command allows you to, likewise, perform special purpose calculations of the diagonal of the Normal matrix. No shell scripts are supplied to access these commands.