> I thought (and the manpages always indicated) that the rule was that /etc/rc and /etc/rc.conf were fair game, and that if you wanted to make changes that weren't overwritten by a system upgrade, to put them in /etc/rc.local and /etc/rc.conf.local. I'm unclear why this is considered a problem.

For the most part that's true, but /etc/rc.local is run fairly late, so if you have a sufficiently-crazy setup you might have to edit /etc/rc.

For example, before softraid crypto was integrated into the bootloader I modified /etc/rc to prompt for the keyphrase before it tried to mount the disks.