Why do academics, in their professional writings, refer to their scholarly predecessors and one another by their surnames only? It may be tempting to answer that that is the convention – “everybody does it”. However, while that is a compelling explanation, it does not constitute a good justification.
Yet it seems that the practice does require a justification because, on the face of it, it appears impolite to refer to people in this way.
Of course, to most people it does not "on the face of it" appear impolite to do this; it's generally regarded as a polite act, which is why people do it. The whole argument is flawed because whether something is polite is in fact a matter of convention; if it's a genuine convention, it's not impolite to do it. If there's a further moral problem, there might be a reason to change the etiquette. But it's utterly, utterly absurd to say that some common practice appears to violate etiquette while refusing to listen to people who point out that, in fact, the etiquette currently involves an expectation of, by and large, engaging in that practice. If everybody does it, it's not rude to do it -- it may be any number of other things, but it is not impolite.
He goes on to say:
Of course there are contexts in which people do address one another in precisely this fashion. The military, as well as traditional British public schools come to mind. However, while these are environments of formality (which explains the more respectful ways in which “superiors” are addressed in those contexts), they are also de-individualising and harsh cultures. They are thus not the touchstone of politeness.
Whether anyone thinks the lives of an entire segment of the population is "de-individualising and harsh" is, of course, utterly irrelevant to whether something is polite and courteous in an entirely different domain. Courtesies are not something any one person can arbitrarily dictate to other people; they are something we are doing together, and thus they are culture-relative. The culture within which you are operating matters. Academia is a culture in which the expectation for politeness is that you will, by and large, refer to living people by last name in formal writing, and in informal writing where reputational or professional concerns are relevant. Using first names in a journal article, for instance, will often be read as patronizing or condescending. Using professional titles in such a case is usually acceptable, but in most situations not regarded as necessary for showing professional respect, and contrary to the argument given at the link, people do often find a consistent use of titles distracting, as overformalizing the discussion; you would usually only do it when you had reason to emphasize their credentials explicitly. Something like that is the usual practice, although people are not usually bothered by occasional deviations and different contexts may allow wider and more common deviations; but, regardless of what is usual, the usual practice is the standard by which we assess whether something is too informal or overly formal.
It was just last year that I discussed a fairly widely shared post that insisted that Princess Elisabeth should be referred to by her last name because referring to her by her first name was disrespectful, and that referring to her by her title made it sound like she wasn't a real philosopher; as I noted then, neither was true of actual practice, and making these things a general rule for historical figures would be insufficiently flexible. Some philosophers have a tendency, one fears, to try to universalize their private preferences; here we have two people universalizing their preferences in different directions, and both absurdly. What we learn from the article is that David Benatar has an opinion, and not really anything more; what we learn from the usual practice is that most people do not in fact share that opinion. And it is frankly a bit arrogant for him to think that everyone does. I'm from an area of the U.S., for instance, in which his preferred practices, using someone's first and last name, or their title and their last name, in a context in which you are criticizing them often sounds like you regard yourself as having a right to reprimand them -- the former is what parents do when their children are in trouble and what teachers do when students misbehave, and the latter is what you do when regard yourself as having the right to rebuke someone over whom you don't have authority. (It's not usually a problem where there's no criticism at all, although it will sometimes sound stilted.) If there are situations where it's obviously the custom, that custom overrides in those situations. On an individual basis, you can come to a mutually accepted result, and people will usually try to accommodate revealed preferences if they aren't too troublesome to accommodate. And, of course, different customs prevail elsewhere. Probably no one would have a problem with David Benatar doing it if they knew why, regardless of their usual way of doing things. But it's not an a priori truth that his preferred way of doing things is more polite than what other people actually do, and he doesn't really have the right just to assume that it is.
It's entirely right, of course, that we could do things differently. We could do things any number of ways differently. That's why no one is likely to be very bothered by Dr. Benatar's highly presumptuous way of arguing -- we could indeed do it his way, and one could very well be of his opinion that it would be a better way. But the possibility of having a different etiquette is not relevant to determining what the etiquette is. As I pointed out above, we may have reason to think that some other way of expressing courtesy and politeness would be better for some more fundamental moral reason, but if you want to know what's polite, you ask what people of good will usually in fact do, and when you know that, your question is answered. And if you feel that it is impolite, if you mean that literally and not as shorthand for simply saying that it would be regarded as impolite in a morally better system, you are provably wrong. If you want to know whether something is legal, you look at the code and precedent; if you want to know whether something is polite, you look at common rules of thumb and customs. It's a very serious error to confuse what's legal with what you think should be legal, and it's at least something of an error to confuse what's actually polite with what you would prefer to be counted as polite.