I setup an
automatic installer for linux, which I attempted to port over to OSX as well, but I can't really test it.

The full set of scripts is at
https://github.com/eli-schwartz/calibre-installer/ if you want to check it out.
One thing it does is symlinks the CLI tools into /usr/bin (because whyever not, if you are running a root script to update calibre, rather than copying a .dmg via the GUI?)
calibre used to do that in Preferences ==> Miscellaneous, but apparently the method used stopped working.