Migrating macports from a backup location
It seems that the location can only be set when compiling macports from source (using the --prefix option).

Rather than going down that route, I copied my old macports directory from the backup location to /opt, I then re-ran the current macports installer, which overwrites the "darwin 13" binaries and updates the database file. Following this I was able to follow the steps in the migration instructions to reinstall all ports.