> @sample etc/newsyslog.conf.d/zrepl.conf.sample
is certainly wrong, because all files in etc/newsyslog.conf.d/ are executed.
Sample should be under %%ETCDIR%%, something like
> @sample %%ETCDIR%%/newsyslog.conf.sample etc/newsyslog.conf.d/%%PORTNAME%%.conf
> @sample etc/syslog.d/zrepl.conf.sample
likely suffers from the same problem.
I have modified the FreeBSD base default newsyslog.conf file to only include files which end in a .conf. This will take effect from FreeBSD 13.