I noticed that despite the settings new users were not being auto-subscribed. Digging further, the users in question were missing the wp_2_s2_authors meta_key in the wp_usermeta table. This is a multisite instance of WordPress. It would seem that the register() function in class-s2-core.php is not setting the usermeta values when new users are added.
Also, the site is using a SAML plugin to handle login/registration. If a user authenticates but does not exist in WordPress, they are added with the wp_insert_user function.