Well, the question of which libglx.so is loaded by applications is determined by your shell environment, not by the X server itself (this makes sense when you consider that X11 was designed to be able to display applications running on a remote machine).
So, assuming that your xorg
libglx.so is under
/usr/X11R6/lib and that for your nvidia cards is under
/usr/X11R6/lib/nvidia then you can do:
# for the nvidia drivers
env LD_LIBRARY_PATH=/usr/X11R6/lib/nvidia quake3
# for the Radeon version:
env LD_LIBRARY_PATH=/usr/X11R6/lib quake3
But that said, my reading of your X11 configuration states that you're not using Xinerama, but instead using separate screens that you (AFAICS) migrate windows between. Assuming that's true, then you won't have a problem.
Otherwise, I can potentially imagine a great deal of confusion happening when an an application which has the radeon glx drivers loaded starts up on the nvidia head.