Easiest way to remember is that any settings done in Windows or a graphics utility like Nvidia panel, CCC, Rivatuner, ATTray tools, are making adjustments at the driver level - think of the driver level as %root on a computer.
This then begs the question why do games have settings at all when you can default to the driver level? A) Because not many people know where to go and adjust these features, beyond the in-game menus and B) Some games are coded and programmed to either ignore driver level adjustments or to disable them.
Most driver level features we are used to modifying i.e. AA, AF, LOD scaling, Mipmap quality, etc. no longer respond in a 3d program due to the way DirectX and OpenGL versions work.
It's very possible that a game will use the driver level settings and the in-game configuration simultaneously. Doing so could cause crashing, compatibility and performance issues. Or the program may recognize both and give one precedence over the other.
A simple example I can think of is L.A. Noire has an in-game anisotropic filtering scenario just like you mentioned with DOOM 3. Turning on 16AF outside of the game IS noticeable in the game, so clearly the game is allowing that higher quality AF.
Here's the way I would approach this.
A) Always remember Hardware > Software e.g. driver level adjustments > in-game adjustments
B) Having settings of hardware and software running together may cause problems, so refer to "A", assuming the program recognizes it.
C) Not all programs will welcomely receive or use the hardware's registry driver level settings.
D) If you have a case where the program seemingly utilizes both, then turn the in-game setting to it's minimum and the hardware/driver level version to the maximum (or your desired setting). If the program has a strange bug or etc, then reversing that and making in-game adjustment higher may work out better.
Awsome game I wish i could get it but parent are fags and they dont't let me get M games.
You didn't call your parents fags
You didn't call yourself "hacker" on the internet
You learned to spell "awesome" and "assassin"
they might think you are mature enough to get the game. -Davidelmo