I was finally curious enough to start power googling this morning for relevant info and so far found the following:
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The A-S801 does use some sort of buffer amp for tone control.
- Could not find any reviews with measurements except for Gene's that I read long time ago and read it again after seeing your post, and he didn't mention anything about direct vs tone control that is relevant to your findings.
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Did find one, with measurements, for the A-S3000, and that one showed a slight level change with tone control on.
By the way, if I remember right, for a good ABX between electronics, it is important to level matched to 0.5 dB. A quick search found the article linked below:
http://www.bostonaudiosociety.org/bas_speaker/abx_testing.htm
In the 2nd paragraph under the "Listening" heading, it says:
"Meyer handed out a sheet photocopied from the ABX manual which showed typical level-matching required for reliable detection of differences between sources with 1/3 octave frequency-response aberrations. When the aberrations span a wider spectrum, level-matching becomes increasingly critical, dropping to less than 1/3 of a dB especially in the ear-sensitive 2-5kHz region. Acuity (ability to hear difference) also depends sometimes on how close to the threshold of hearing the level of the frequency is. At threshold, a small increase in level will make the sound audible and enable the listener reliably to distinguish A and B when different."
I am not ruling out the difference you found is not due to something other than level difference, but I sure hope it is not due to audible distortions or change in FR or other critical criteria that could degrade sound quality. I am somewhat confident that Yamaha should know better not to degrade SQ just because someone needs tone control for whatever reasons.