Further investigation suggests that Dreamwidth is duplicating LJ's behaviour in both respects. I've always had plaintext notifications from LJ, because I like to see people's HTML, but I've switched it to HTML notifications now, which should enable inline replies. Also, I never even realised I had an LJ mail-box, but I do and it gets all the comment notifications. There's no way on either site of getting external email notifications without also getting internal notifications, which seems like a lacuna.

(I've disabled email notifications for people adding me on Dreamwidth, because they were cluttering up my inbox, but I still want to be notified, so it would be nice to use my Dreamwidth mail-box for such things without also having to reread comments I'd already seen. But this is getting boring, and I really should do some work.)