The IMS Enterprise enrolment plugin allows you to create accounts, and set the user's auth type to $CFG->auth
$person->auth = $CFG->auth;
However, since the multiauth changes, $CFG->auth returns a comma-separated list of enabled auth plugins. The effect is, for example, to set mdl_user.auth to 'ldap,manual' rather than one or the other. This means the user cannot log in.
I'm really not sure how to address this. It's not possible to specify the authorisation method in the IMS document; or at least your IMS document wouldn't be compliant anymore.
I've marked this as "Major" because it's going to affect some large institutions come October.