I just encountered the same issue. The main reason seems to be a hard-coded setting in the bootstrap3 plugin.
To make it work with the Cloudron-packaged app:
- add the path
/app/codeto the$doku_inc_dirsarray intemplates/bootstrap3/css.phpandtemplates/bootstrap3/iconify.php - when setting the theme through the DokuWiki Admin panel, the following setting is added to
/conf/local.php:$conf['plugin']['oauthgeneric']['scopes'] = array();`, this prevents login through the Cloudron SSO. Manually remove it and login again.

