Correct. The XBOX GPU is still being patched to output RGB to the encoder in a v1.6 XBOX with my patch, but unfortunately the encoder itself is not being patched. This means that although the GPU is outputting RGB, the encoder is still in it's retail state, which is what prevents it from displaying VGA properly.
Hopefully some documentation on the Xcalibur encoder will emerge, and if that happens I can easily apply the appropriate code to my patcher to support v1.6 XBOXs. (Hey, Microsoft, how about that datasheet?

)
NOTE: The green tint is a direct result of the GPU being patched for RGB, and the encoder not being patched to recieve an RGB signal. This also happens with standard A/V cables too, because the standard cables are not enabling HDTV output (Because they are not HDTV cables...

), and the HDTV code for the encoder is what is actually being patched in my patcher. And also note, that the reason why the colors are incorrect when using an actual HDTV cable and a real HDTV is because the encoder is trying to output VGA colors and signals to an HDTV, and most HDTVs cannot accept a VGA signal on their Component Inputs.
So basically...
Composite (Yellow, White, Red) = Green
S-Video = Green
SCART = Green
Component = Green
Homemade VGA Cable = Beautiful VGA Colors

This is why it is recommended that anyone using my patcher should also have a 'clean' BIOS on the second bank of their modchip for usage on TVs.