Looking at his figures from the Audio Nirvana site, these don't seem to me that they would be in the audible range. Especially trying to hear it over any playback material. Arbitrageur couldn't hear it.
If the EQ circuit was introducing audible noise, wouldn't you be able to hear it with nothing playing by just toggling the EQ on/off? It's something I'll try when I get back home.
No, I don't believe the auto setup changes any of the PEQ settings. I'll check that too.