I'd assume with things like copy/pasted tag lists and whatnot that this is still a pressing enough issue, but apologies if I'm doing too much restating.
Regarding the alerts at the top of the page, tag notifications are less precedent than watched thread notifications when tags' taking precedence would make more sense.
The notification parser is too strict. It seems to only treat spaces as a separator and ignores things that aren't even possible in usernames like non-breaking spaces (so I wouldn't be tagged by @BradinDvorak or @BradinDvorak,). Nbsps have a tendency to crop up in the RTE when something's pasted in there, so the average copy/pasted tag has a decent chance of not working. Don't know the mechanics, of course, but perhaps switching whatever the separator currently is with a word boundary \b or non-word \W would solve it?
EDIT: Okay, one of them actually did tag me, but I was dumb and now I can't be sure which one.