It depends on the context. For example, imagine telling a teenager that their face is covered in acne, or (to use an old example of pg's) telling an old person that they will die soon (https://news.ycombinator.com/item?id=6539403). It's not hard to imagine contexts in which pointing out those facts would be being a jerk.
> you don't need to start a meta-discussion thread, which is itself a discouraged practice
That's true in general. I'm a mod here (sorry if that wasn't clear) and part of my job is to post replies when people are breaking the site guidelines. You're right that such comments are off topic and tediously meta - but it's a form of out-of-band communication that is necessary for keeping the site on-kilter. If it helps at all, these comments are even more tedious to write than they are to read :)
Also if you disapprove, modding down is enough, you don't need to start a meta-discussion thread, which is itself a discouraged practice.