It has to do with the way distortion works: as you add gain, you'll notice changes in frequencies, particularly with respect to bass, which becomes more pronounced the higher the gain is. For the same reason, you'll often find that a clean sound is usually perceived as louder than a distorted.
I lack a detailed explanation, but it's something like this: the lower the frequency, the higher the level must be to achieve the same perceived volume.
I agree with you but it seems like you are saying the opposite of Viabcroce as he was saying that the Vavg (or perceived volume) of a clean sound was LOWER than distorted sound therefore I was over compensating by setting clean sense too high. While you are saying that the clean sound usually is perceived HIGHER than a distorted sound due to the loss of higher frequencies and the bass boost in the gained amp.
So which is it? Also when setting clean sense should one be balancing the Vpeak or Vavg of clean vs distorted? If Viabcroce is correct then it sounds like he is suggesting that Vpeak be balanced where as I am balancing Vavg.
Not sure if it makes much difference in the long run, just so long as the user is happy with the sound is all that matters but it would be interesting to hear what C Kemper has to say.