I never customized it. It contains %{base_url}/u/confirm-new-email/%{email_token} like you advised, but in the actual email there is /authorize-email/ in the link. So I guess something goes wrong between the web admin panel and the some config file deep down in the engine room of Discourse. Running 2.5.0.beta6
Edit: even more strange: when an admin changes email address a confirmation to the old address gets it with %{base_url}/u/confirm-new-email/%{email_token} but the new address gets it with %{base_url}/u/authorize-email/%{email_token}