Mike, you wouldn't find it "difficult to believe" that none of these processing features could possibly have an effect in a "direct" type of mode if you fully took into account the fact that the processing features are totally bypassed in that mode.

As to the effect of the pre-amplifying section as distinguished from the amplifying section, certainly that's in no way being overlooked, either here or in the test labs. If you check the lab tests on receivers run by Sound&Vision and HomeTheater Magazine, you'll note that they test with the various low-level inputs in use, so therefore the audibly transparent results that they've measured include the effect of both the pre-amplifier and amplifier in the receiver.

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Enjoy the music, not the equipment.