Update:
The issue seems to be specific to the latest release of Dokuwiki and the plugin. When I use the oldstable version of the wiki, the plugin displays the "Twofactor Settings" link in the upper right corner of each page. When I upgrade to Greebo, the link vanishes, and I can't set any preferences.
I have filed a bug on Github:
https://github.com/wilminator/dokuwiki-plugin-twofactor/issues/9