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/code to the $doku_inc_dirs array in templates/bootstrap3/css.php and templates/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.