I know there's no concept of marking profile posts and comments as "read" at the moment and it's probably a bit trickier to do it due to the presentation of the content and maybe overkill, but if some solution could be put in place to prevent all these duplicate alerts it would be better than being flooded like we are now.
One possible solution is a simple check before the alert is generated:
SELECT view_date FROM xf_user_alert WHERE alerted_user_id = ? AND content_type = 'profile_post' AND action = 'comment_other_commenter' AND content_id = ? ORDER BY event_date DESC LIMIT 1
Finally, the alert phrase should have "There may be more comments after this." to be consistent with posts.