It shouldn't be producing both.
I filed this issue some time ago but it was never addressed:
Timeseries files for both MOSART and RTM are being generated · Issue #213 · NCAR/CESM_postprocessing
Both MOSART and RTM (the runoff models) timeseries files are being generated for CMIP6 cases despite the fact that only MOSART was run in the simulation. For example, I see only MOSART h0 files her...github.com