[quote=@Shienvien]
Oh, and what about the quote/quotemention matter (as right now, the only way to make "normal" quotes is to remove the '@' by hand or type the name in manually)? I'd rather avoid sending unnecessary mentions, since with threads that will be browsed by the person anyway, it just means they will have to separately go to the alert tab to dismiss the alert.
[/quote]
I think you should just quote-mention. Clicking in to a quote-mention from the notifications menu clears it. Though I need to improve notification auto-clearing and allow users to delete specific notifications from the list. But altogether I think it's better to err on the extraneous side.

Eventually notifications will be auto-cleared when you view the page of a topic that created them, so it won't even be an issue. And I expect most people are happy to see a number next to the bell icon even if they were gonna check the topic anyways. I personally use notifications as a to-do list and often forget to respond to posts that don't notify me, so perhaps other people are similar.