What is the correct way to handle role permission manager and bench update conflict


I need a best practice to handle this task.
I just start working role permission manager recently and able to control security access by different role and perm level.

however, once I go to bench update (I am using 13-dev), it will always show file conflicts.
yes for sure I can use git add / git stash to pass update and restore back what I change, but is that the correct way to handle this?