This is not always the case and depending on several factors (placement of FR/FL , source material and room treatments) the bypass can indeed be a very useful feature when using a sub and only want to correct the bass in said sub . while the many different options that exist at one's fingertips can be daunting at times ,it will always comes down to what sounds best to you and you alone. for instance the "dogma" surrounding using the Mains+ sub feature for music is IMHO handy at times when you just simply want more weight period , this coupled with DEQ with a offset of 5 with full Auydyssey correction can indeed sound fantastic if your setup is not producing boomy bass from the get go of course (good subs and mains do help) Now as for all the talk about Audyssey and music in general is interesting to say the least, and my findings have been nothing short of stellar with multi/ch sacd especially with my reference collection of classical ! i know these disc well and have come from listening to them mostly in 2/ch DSD (no conversion,Auydyssey or bass mngt or distance settings in the chain) and of course the switch there respective multi/ch versions with Audyssey (no mains +sub, just the calibration results incarnate) and yes even DEQ at 5 or 0 or off ,are some of the best playback experiences I've ever had even with the down sampling done in my Marantz 8801 as for regular CD's and hires files , Pandora, Youtube or all else Audyssey can deliver the goods if and only if its done right.
There are no right or wrongs here period! and the final result must always be done by your ears or what's the point at all
I hear you and I understand if people like it