I believe we'd had a similar discussion before!
In order to use audessey, you've got to run the automatic setup. The way the setup detects the speaker positions and room accoustics would then determine on how accurate it calibrates the volume and equalizers. This depends on various factors which may or may not be in our control.
I've not used Auddessey but manual setup. My setup resulted in a weak bass and unrealistic volume levels. I'd then adjusted the Bass/Treble and equalizers to suit the normal listening volume manually and the results are magnificent!
In any case, to listen to music or movie in a natural form, all artificial components should be removed as any bass/treble or equalizer does boost/cut of frequencies resulting in an unnatural sound.
I feel these controls are/were used in cheaper audio/video systems whose amps do not respond well to bass frequencies less than 100Hz or treble frequencies above 10Khz, hence the controls levereged the amp incabability and the listener would feel great.
However, because most AVRs do well in the entire audio spectrum, the use of loudness, bass/treble or equalizers should be at minimum or avoided.
I would wish to stress that the speakers used, especially the fronts, center & sub-woofer should be matching in power & efficiency. Else a huge mismatch would be observed, as the subwoofer should cover the lower bass frequencies while the fronts should cover the normal bass & treble while the center handles the voice sound stage. If the power, efficiency and sizes mismatch, then the overal audio quality would be horrible, making us tweak the system unnecessarily.