The Windows 10 fix is automatically aplied when the game is started. The same is true for everything that the game optimizer did before this release. It is now integrated in the core app.
FO3 specifically: incidentally I checked the game earlier today to do the hotfix linked above. All I can say is that there definitely is no general issue with the game. What you could try is checking the “Never change any game settings” checkbox in the config app. That’s the only thing that has really changed in regard to FO3 from the last release.