Maniphest notifications are mostly atomic (one action triggers one mail). I appreciate that because I can filter notification emails I am (not) interested in based on the subject line. However, this is not the case for adding comments. While only adding a comment triggers an email with the subject
[Commented On] T12345: Example
it is also possible to have another action (refered to in the subject) and adding a comment (not refered to in the mail subject but only in the mail content):
[Changed CC] T12345: Example JohnDoe added a subscriber: JohnDoe. JohnDoe added a comment.
I'm not sure if splitting this into two emails is technically feasible and wanted; It might be easier to enhance the subject to mention both actions:
[Changed CC] [Commented On] T12345: Example
(Also brought up by a user in http://fab.wmflabs.org/T147)