I'm somewhat amused at this post at the APA Blog. I want to be sympathetic to the general point, but it's difficult to take seriously when the author keeps referring to Princess Elisabeth of the Palatinate as "Bohemia". When we call her Princess Elisabeth of Bohemia, "Bohemia" is not her name; it's the name of a kingdom and part of her royal style. We call her Princess Elisabeth of Bohemia because her father, the Elector Palatine, was for a very short period the reigning King of Bohemia. It's as if someone in the future were to insist on calling Queen Elizabeth II, "Great Britain". Besides the absurdity just on the face, it is, frankly, ridiculously absurd to think you are affirming a woman's agency by calling her the name of the kingdom her father happened to rule until he lost it.
If you really were insisting on using her last name, I suppose the proper name would be Pfalz-Simmern, which is the name of her House. But it doesn't make all that much sense to do so. For one thing, that's not how she would generally have been known, nor the form of address she would have expected from other people. She would just have been Princess Elisabeth, and, later, Princess-Abbess Elisabeth, and anything else would have been just to clarify if there might be confusion with other people of similar name. For another, she is known the world over as Princess Elisabeth, and it does her no great service to pin her with a more obscure one.
In addition, despite the author's assumption that it is the standard to use a person's last name, the field of philosophy has no ability to apply that standard rigorously. 'Novalis' is a pen name; 'Plato' seems to be a nickname (according to one line of ancient rumor, his real name may have been Aristocles, but we don't even know for sure); 'Aquinas' is not St. Thomas's last name but literally just means 'the guy from Aquino'; 'Marcus Aurelius' is just the name that ended up sticking to the man who was known at various times of his life as Marcus Catilius Severus, Marcus Annius Verus, and Marcus Aurelius Antoninus Augustus (I suppose if you were to insist on last names, 'Augustus' would be the closest thing). We call Anthony Ashley Cooper 'Shaftesbury' because he was, in fact, Lord Shaftesbury. Calling Damaris Cudworth, 'Cudworth' invites confusion with her father, who is better known under that name; since she was Lady Masham, she's often called that, or, more often, Masham. There is no standard of using last names in philosophy; there can't be. What is typically done is to use the name most convenient for distinctive identification -- which happens to be the last name through most of the West for a good portion of the past several centuries because of the spreading popularity of [first name / family name] as a distinctive identifier.
If we are really concerned with agency, I would go in exactly the opposite direction that the author of the post does: instead of dropping titles and using 'last names', in formal contexts we should in fact show respect by at least occasionally using the highest title applicable to them unless they themselves chose to call themselves something different. Thus 'Novalis', 'Lord Shaftesbury', 'Lady Masham', 'Lady Mary Shepherd', 'St. Thomas'. It's disingenuous to say that you are respecting (say) Lady Masham's agency by calling her 'Cudworth', when that would in fact have been taking an immense liberty. It's natural that in informal contexts people will use shortcuts like this, but in formal contexts, a little respect, applied at least sometimes, makes sense. (I grant, though, that most people would balk at 'Imperator Caesar Marcus Aurelius Antoninus Augustus'. It's probably impossible to get perfect consistency out of people.)
It's noticeable that assigning people last names sometimes gives results that are exactly the opposite of what is claimed: 'Shepherd' collapses Lady Mary Shepherd's name to the part that belonged to her husband. Again, there's no problem with that as shorthand -- there are fewer Shepherds than Lady Marys she might be confused with -- but if you really are concerned about this, you should call her, in full, 'Lady Mary Shepherd'. That's how she signed her letters. That's what pretty much everyone called her whenever they talked about her. If recognizing her agency is the issue in question, it's absurd to say that anything else is superior specifically in terms of recognizing her agency. It is nonsense to think you are especially respecting a woman by stripping her name of signs of respect she's historically had.