I have added a command that runs "hd-idle". It seems to need to run as root as otherwise it does not spin down the drives as instructed. Behavior seems to be the same when executed manually or via rc.local. hd-idle was compiled with make install as opposed to installed with apt-get if it matters.
From another question on this site I know rc.local runs as root, so why do I still need to add sudo for my hd-idle to run?
Last 2 lines of rc.local:
sudo hd-idle -i 300 exit 0;
The above rc.local works as expected and the hard drives go into stand by mode after 300 seconds. If I remove "sudo" and reboot the hard drives never spin down.