The well-known is usually served up by the main domain (example.com) so for a start if your nextcloud is installed on a subdomain, the well-known needs to be configured outside this nextcloud instance. So make sure to have an app installed at example.com so it gets routed to Cloudron. Then you can configure this via https://docs.cloudron.io/domains#well-known-locations
Though not exactly sure if this nextcloud app would expect the same things as mastodon, but you can try to set the well-known mastodon accordingly, maybe that works. Otherwise we may have to add support for whatever this needs.