I don't fully agree with the premise of the Question, that "we tell users to comment when they don't have sufficient rep to do so". It clearly states the limitations on Commenting, as a privilege to be earned via reputation building.
One can argue that this restriction is undesirable for policy reasons, but that is a different discussion, one that has been held on Meta.SE as well as many Community Meta sites. If new users are motivated at all to earn this privilege by participation in constructive ways, that aspect of the templated text is serving a useful and encouraging purpose.
There are some corner cases where "comments-as-answers" are worthy of being transformed (by a Moderator) into actual Comments (one can and should flag for Moderator attention in those rare cases). But often the posts that get deleted with an explanation that it isn't an answer but (possibly) a comment instead are simply failed efforts at providing useful answers.
Thus the primary message of the templated text is giving the OP a sense of which way they have failed in using the Answer box on this site.
Further this particular message is only a template, and an optional one from a list of several available to a Reviewer. That is, the No Comment option is the default, and since the message is posted as a Comment under the Reviewer's username, it is editable for an interval of time after posting, and it can be deleted by them at any time.