I was upgrading a system from 11.2 to 12.1, and freebsd-update presented me with a diff removing the /usr/libexec/atrun line from /etc/crontab. I wasn't sure whether to accept this change, so I RTFM and see that atrun(8) still says:
The system crontab(5) file /etc/crontab must contain the line
*/5 * * * * root /usr/libexec/atrun
so atrun is invoked every five minutes.
This makes removing the line seem like an incorrect change; however, I looked through the svn history of the crontab file and see that r318443 removed this line and put it in /etc/cron.d/at instead.
The man page should be updated to reflect this, but I don't know what the best wording is. Perhaps something like "The system crontab(5) segment /etc/cron.d/at must contain the line"?
Additionally, crontab(5) does not mention cron.d at all. Would merging the "Jobs in /etc/cron.d/" and "EXAMPLE OF A JOB IN /etc/cron.d/job" sections of cronie's man page  be appropriate? It's clearly derived from the same Vixie cron man page and is ISC-licensed.