For posterity, I will keep posting here until I find a solution that works.
I had a look at the github site and found the https://github.com/freedombox/FreedomBox/blob/master/plinth/modules/calibre/data/lib/systemd/system/calibre-server-freedombox.service file. on the box it is located at /usr/lib/systemd/calibre-server-freedombox.service. It also had a setting for default library and a home directory.
However, after a systemctl daemon-reload, and a systemctl restart calibre-server-freedombox. I only seem to have broken the server. Returned settings to normal for now.