The need for triple buffering stems from the fact that the PC version was rushed and lazily ported, effectively getting a 30 FPS cap in the process, due to consoles tanking on any higher frame rates on a lot of graphic intense games. Another game with same problem is NFS Rivals.
Me, I just make a profile in D3DO and launch it via an easy one click custom taskbar toolbar. You really only need to set it up once, then it's just one click (after you open the toolbar).
On the CPU Affinity thing, I'm sure you mean cores vs CPU, and it's common that a lot of games load up heavier on the first core. It's getting better though as games evolve.
As far as avoiding using D3DO, you do have the option of making a profile for using Triple Buffering on a specific game in your GPU's control panel. Then when you launch the game, it will automatically use those settings, then revert to the norm when exiting the game.
I have tried forcing such settings via Nvidia Control Panel, Catalyst Control Center, and RadeonPro though, and none of them are as efficient FPS wise as D3DO. I doubt Nvidia Inspector is any better either. So basically, on TB, you are already using the best method.
Just be glad D3DO even exists. It's a 3rd party freebie gem, just like VirtualDub.