Legitimate notifications from web apps are still useful. (e.g. being mentioned in real-time chat) The problem is the rampant spamming of the permissions prompt

Legitimate notifications from web apps are still useful. (e.g. being mentioned in real-time chat) The problem is the rampant spamming of the permissions prompt itself and ensuing inadvertent acceptance. So the practical solution is to close that vector. Instead of the active popup, use only a passive menu entry or an unobtrusive icon, like how it already works for mailto handler registration.