Applying the activation link to linked text in the notification email
Probably this has been fixed since this old question, but just wrapping {{link}} variable in &lt;a&gt; tag lets me send custom HTML notifications with working clickable text links.

Screenshot of messages settings:



Screenshot of custom HTML email received:



Perhaps this won't work for the text version of the email, but if needed I suggest you to use this excellent plugin which let you send custom notifications in both HTML and text versions: Sprout Emails.