top-level posts should not have any special status at the protocol level other than not having a parent.

Those are implementation details. The point is that top-level or parent-less posts have a special semantic status: they start a new conversation.

I also dislike private messaging systems -- not so much because they shouldn't exist, but because they should be implemented as email accounts that only deliver mail among local users, so you can handle them in your regular email client if you want.

It's a matter of integration: I want the same settings, and client software, that you use for the rest of the forum to apply to privmsgs. For instance, blocking a user's messages, sending privmsgs as replies to forum threads (and displaying that correctly in the client), ...

And I don't want to have to use two different client applications at the same time (email & forum) for private vs public messages.

And most people only use webmail, and you can't tell gmail.com to display messages that live on the lesswrong.com IMAP server, if that's what you intended.