Some decent coding could neuter it when totally covered, or minimize usage, whether you have a maximized or a Full Screen app running. A lot of games go Full Screen, and most AV detect this and tone themselves down. But if my desktop PC is sitting there idle with all my Windows minimized, why would I not want to get mail notifications in a way that doesn't involve popup spam that is bigger than the OSX stuff? That is much more useful than shoehorning them into the Start Menu on the side, which I'm going to ignore because if I opened the Start Menu I'm dead focused on opening something specific.
Magnet links theoretically support SHA-1 hashes, so in theory you could craft a magnet link with that hash and see if anything comes up, but in practice they rarely ever use SHA-1 hashes, so I don't know if this would work 100%