You are not bypassing the Sony dac, that is not possible to do. The first thing that happens on the analog in is that the signal is converted to digital.
Actually I knew this but has forgotten. Regardless I still seem to get a clearer, more etched signal with the Qutest than going straight in with USB…logically the cleanest should be sending the source direct digital but doesn’t work out that way to my ears.
You can still get a different sound (ie, the sound of another DAC) by using the analog out of that dac and using the analog in. It gets redigitized because of how the amp is designed, (The entire S-Master circuit) but that is fine, it doesn't mean it will lose the character of the analog source completely (although it will change it - in the case of Chord warming things up a lot). I suggest re-digitizing analog sources to DSD 11.2 for best results. It does behave like an amp still, ie, you can't apply any of the DSEE filters or DC Phase Linearizer this way as it is bypassing part of the internal circuitry.
Yes, it's not a pure analog pass-through, but don't let it stop you. I usually use it in combo with my Hugo2 and enjoy it. I spent a lot of time handwringing that this was "not clean" but this machine is designed to do it this way and it sounds great. Use your ears sometimes over technical specs or what you think you "should do" from dogma, IMO.
I would suggest using the 3V line level output for best results on the Chord device as well. I assume the Qutest has this. it is a special mode that can be activated on Hugo2. That is also something that is non-standard (higher than normal 2V) but yields great results.
I've been using the TA-ZH1ES with this configuration for many years, no issues. the only thing is the display 11.2 Mhz > 11.2 Mhz is a little weird. It "reads" like you're getting a DSD signal from the Hugo over the RCAs. but that's clearly not what's happening. Anyway, I guess they can't display Analog > 11.2 Mhz out of a quirk of the display.
One advantage of the Hugo2 is it has it's own headphone amp so I can compare it's "pure sound" vs with the TA. With the TA is much more enjoyable IMO, although I use both from time to time, usually when I'm using the Hugo2 in bed. It's a better DAC imo, although the TA-ZH1ES is no slouch -it's just more relaxed and a different, sony house sound vibe.
Think of it this way if you're still concerned about doing this. People often prefer the sound of a boutique, hand made, 5,000 dollar ( or much more) Tube Amp over solid state amps that are much more technically proficient. They sometimes prefer ladder dac technology over sigma delta or custom FPGA designs. So it's not all about what is "technically the best" or "technically the cleanest" when it comes to sound. Is it ? It's just about what sounds good to you.