Of course, you might have been testing traction control under low speed/throttle and that is less affected by the change compared higher speed/throttle. Who knows. I have seen it written several times that the secondary butterflies *are* used by the traction control system, but it is only part of it (the primary method being fuel control). They are likely primarily used to "smooth out" the throttle response to increase drivability. The "flies" give the computer some control over air intake.
Yes, the conditions I reported above were at slow speed, but I don't think the system works differently at higher speeds or with larger throttle inputs. The TRC is supposed to sense rear wheel slipping due to loss of friction and vitiate torque to that wheel relative to the same throttle input without any slippage. At least, that's how I understand it.
So when I was driving through the gravel, I maintained the same basic throttle input, and the computer kept the rear wheel churning as necessary to keep the bike moving, even though it was bogging down to different degrees depending on the how deep the gravel was. It appeared not to be effected by the fly removal. and I don't see why it would be different if I were to be moving at a higher speed.