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rgsrmfgen generates the response matrices. These are required by rgsfluxer for fluxing spectra, but their true value is seen in such sophisticated analysis packages as XSPEC, where a resolution of 3000 to 5000 incident energy bins (parameter rmfbins) is recommended for good results. Unfortunately such large matrices take a lot of time to compute--massive overkill if used only for fluxing. The default resolution is set high to avoid misleading the unwary, but lowering it to rmfbins=250 is highly recommended when fluxing is the only use intended. Similarly, the default for parameter fftdim is adequate for any purposes, but fftdim=1 is faster and not too crude for fluxing (this parameter controls losses due to truncation at the wings of various distributions used in computing the response).
Strictly speaking, the spectrum for a given exposure should be paired only with a response matrix generated on the same exposure. However, this stage produces only one response matrix per instrument and order, selecting one exposure somewhat arbitrarily. This is probably acceptable even for the purpose of serious analysis. The file name of the response matrix indicates which exposure it actually represents. Finally, these response matrices apply only to the primary source.