As far as I can tell, Jeff, who created Stack Overflow from scratch, was fanatic about protecting the users from unnecessary notifications and emails. For him, and for many others, too many notifications and/or emails would be distracting and disruptive. No personal messages, no instant emails.
I believe this is the reason behind not allowing more than one possible notification (except OP) in a single comment. If the comments system would have been built these days, with the current team, there is good chance we could have pinged more than one user in one comment.
Personally, I'm quite neutral on this. Notifications don't bother me, but I do understand those who are bothered by too many notifications, so I won't support changing the current behavior.
As for chat, which does allow pinging as many users as we want in a single message, it's much more flexible, and those taking part should expect many notifications. So everything written above isn't relevant for chat.