Upgraded thrust bearings are a completely mute point. As at that point the channel would have eroded just enough to cause the exact same thing to happen again. A custom machine shop could bore and custom make bearings, but at that point you are stripping and pulling apart a MQB engine. Which is not cheap nor easy. Which means you should just throw an IE short block on a good core anyway.
It's not an issue you can, should or would worry about until it happens. There's nothing to avoid or cause it so just enjoy your car. If you have a 7/14 build date 15 MT maybe start shopping for a dsg, other than that don't worry about it.