I don't understand the want for modifying the appliance
No doubt he's used to running an actual server and having certain tools available. It isn't the FreeNAS way, but if he has experience elsewhere this doesn't strike me as a particularly bizarre desire. Nonetheless, using a jail is of course the correct answer.
@David Dyer-Bennet, to expand a little on my previous answer, FreeBSD had a change a while back in package managers.
pkg_add was a tool to work with the old system, while
pkg is the command for the new system. The section you quoted from the manual was saying not to use the old system, because it would mess up the package database for the new system. Inside a new jail, these commands will get emacs installed for you:
Code:
pkg update
pkg upgrade
pkg install emacs-nox11
...then mount /var/log as storage to that jail under whatever mountpoint you want to place it.