The graphics package can handle multiple verifying reference dataset for model space verification (i.e., https://github.com/JCSDA-internal/mpas-jedi/pull/1096).
However, this capability is not integrated within MPAS-Workflow. The specification of -R {GFS or ERA5 or EC} should be applied when the statistics are generated, which is ... verifymodel task of MPAS-Workflow.
FYI:
As @ibanos90 suspected, simply specifying -R {GFS or ERA5 or EC} at the plotting step would not work because the statistics file itself contains the definition of reference dataset. For example, I see axis1_level3 = "log_mogfsan", "mmgfsan" ; from stats_mpas.h5 file.