Sadly, Nvidia doesn't give us anything in NVAPI related to Compatibility Mode. The regular Stereo API calls only work for regular 3D Vision.

However! There is a way now!!!

What does this tool do:
Patches in Real-Time (Code Injection) the "UDM" Nvidia Driver responsible for 3D Vision Compatibility Mode (Stereo Reprojection based on the Depth Buffer).
Removes the limit for Stereo Separation (Depth Override).
Adds key shortcuts to quickly jump from one Separation value to another.
Adds key shortcuts to quickly jump from one Convergence value to another.
DOESN'T MODIFY the EXE of the application/game! (It should be safe, with Anti-Cheat programs)
Allows updating the 3D Vision Compatibility Profile (for the application/game).
Supports both 32-bits (x86) and 64-bits (x64) applications.

Do you want to see screenshots? Or to discuss? Let's do it on GeForce Forums thread!

Current Public Release Version 1.0.19

Download: 3D Vision CM "Unleashed" v.1.0.19
Download: 3D Vision CM "Unleashed" v.1.0.18
Download: 3D Vision CM "Unleashed" v.1.0.16