in descr_sm_factions.txt
change
faction empire_west, shadowed_by empire_west_rebels
to
faction empire_west
and
faction empire_west_rebels, shadowing empire_west
to
faction empire_west_rebels
i.e. just get rid of the shadowing bit for those two factions - then they'll act normally and you can add empire_west_rebels in as a playable faction in descr_strat and do what you want with them.