AV Pre/Processor vs 2 Channel Pre-Amp - Sound Quality

A comment on your desired configuration.  If you are intending to run RCA/XLR to the subwoofer first, then take the high-pass output and connect it to your amazing 2-channel amp for bookshelves, you will probably not get any benefit from a dedicated preamp.  The analog stages in the subwoofer that crossover and output the high frequencies are not going to be as good as those found in 2-channel preamp, and even some high end HT Processors (such as the Classe SSP or Sigma).  You're pretty much degrading the sound quality by using the sub as a crossover/preamp for the amplifier.

If you really want a subwoofer and a dedicated 2-channel preamp, I would suggest using XLR output to go directly to your amp/bookshelves, then use the RCA output to go to the subwoofer to "support the low octave that bookshelves cannot reproduce".  It's not a perfect solution, but much better than your original thoughts.  The small bookshelves are going to roll off the bass frequencies anyways.

Oh, for integrated amp that has HT bypass.  The idea of an "HT bypass" is to completely bypass anything in the preamp, including any tone management or crossover.  The unit will typically connect the input wiring directly to the output wiring and not even go through the preamp stage, therefore letting the source AVR or HT Processor do the bass management on its own.

However, there is an existing solution that might help you.  The Parasound units, both the integrated and the P5 / P6 / P7 preamps, have a bass management crossover as well as full HT Bypass for left/right and subwoofer channels.  This allows you to still use a AVR or HT Processor and connect the 3 left/right/sub outputs directly to the Parasound unit for straight passthrough.

The Parasound integrated is a combination of the P5/P6 preamp and a version of the A23 amp with a larger transformer.  The Parasound amps have a warm sounding sonic signature (definitely on the warm side of neutral).  For the preamps, the P7 is the best unit due to better analog circuits and better power supply.

When you use the Parasound units for normal 2-channel listening (such as from a DAC or turntable), the Parasound unit will do the bass crossover management and send separate signals on the left/right and subwoofer outputs.  This gives you the best resolution possible.