My reply to Joshua would be, "try it and see if it is applied".

Every DP is different in how effects are handled; when I use Pianoteq to generate the sound when playing my Roland, none of the Roland controls have any effect on the sound - even the volume knob is disabled - I have to use the volume slider in Pianoteq, or the sliders on my sound card.

What is iAFC?

Supposedly it is DSP which uses microphones to adjust the speaker output for room compensation, produce spatial effects and mimic resonances such as when a singer standing near an open lid of a grand causes resonances within the piano.

I suppose the answer to the question would be "depends whether the piano can be used as a midi controller to PQ, and the laptop output fed back through the line-in of the Clavinova and whether the line-in is affected by iAFC, which seems unlikely."  I can't imagine Yamaha would bother including the feature of "Play your IPod as if it was connected to a Grand Piano."  Or maybe they would!