Uh! Out of curiosity, what does the notification look like in your web notifications?

The email body says Herald added a comment.
The email subject line header says [Changed Project Column] (not [Commented On]).
So I wouldn't say it is incorrectly attributed.
AFAIK there are no Herald rules which trigger a separate email notification on its own (but I agree that the described behavior also has confused me in the past) as Herald rules are always triggered by some other previous action.

In my opinion this is not something to change. If someone wanted to look into this, then getTitle() in https://we.phorge.it/source/phorge/browse/master/src/applications/transactions/storage/PhabricatorApplicationTransaction.php could likely check if ($this->getMetadataValue('herald:transcriptID')), as a condition to start with