Small point, The netherese are not extinct. Not every Netherese arcanist was on Thulthanthar when it crashed into Myth Drannor ~14 years before the events of the game
At the very least, textually, there is a Netherese Lord in the host tower of the arcane in luskan, and there is a coven of Netherese Sorceresses in Anauroch. Presumably there are other Netherese wizards in Anauroch, Telamont wouldn't have trusted all of them to go on his great crusade with him - there were also many survivors of Thultanthar that teleported away or were on the ground on various assignments all over Faerun
Good points! The only thing is that Karus' Folly with Mystril was -339 DR and BG is 1494. The Time of Troubles was more than a century ago when Mystra was destroyed by Helm and yet a new Mystra took the mantle. The Netherese, as far as anyone has known them, have been gone for quite some time. The reappearance of Thulthanthar and its destruction were a relatively quick blip on that map. You're right that some probably exist out there, but not in the sense of "The Netherese" or its empire. You can't go find or visit them or anything as a people. I think there is one city left out in the wild still though? Probably still jet setting around the Astral Sea plotting devious things.