More specifically, mergemaster(8) never touches anything under /usr/local and that means it won't touch the configuration files used by ports/packages. It is only for /etc/* and a few other system configuration files under /, /root and /var.
The only thing to take note of when running mergemaster(8) is /etc/master.passwd that contains the system user accounts but also the user accounts added by ports/packages. Make sure you review the changes carefully if there is a need to do any merging on /etc/master.passwd, mergemaster(8) offers an option to view the results of the merge before actually committing the results.
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