The r4ss issue r4ss/r4ss#460 "create a single function for running SS models for use in r4ss, SSMSE, and ss3sim" has been resolved thanks to PR r4ss/r4ss#722 so the modified functions are available for use in SSMSE. I'm not sure it's worth making changes here if the status-quo functions are working, but future developments could consider moving to the new r4ss functions.
Note this is a repeat of ss3sim/ss3sim#385.