Schiit Freya & Schiit Freya+ preamp does have HT bypass option in passive mode. It is true that it is very rare to see a dedicated Preamp supporting HT bypass.
Freya/Freya+ has 3 Modes of Preamplifier function. 1. Passive 2. JFET Active ( Solid State) 3. Tube Active mode.
It doesn't have a HT bypass mode, the Volume control cannot be bypassed. Passive mode is very close to pure direct but volume control cannot be bypassed, so its not the same as HT bypass.
BTW, I don't think this has any bearing with what OP is asking. His Denon x1400 doesn't have front preouts, so he's better off buying a separate Integrated Amplifier for Stereo listening, along with a decent Source or DAC. Unfortunately he has to switch speaker cables each time he wants to toggle between stereo and HT using the same front speakers.
If for some reason he's not going that route, he could try few remedies.
1. Room treatment for front speakers, focused on Stereo listening
2. Carefully Repositioning the Front speakers to get the best stereo image and dynamics (millimeter perfect)
3. Running Audessey with only 2 Channels being connected and optimizing it further ( he should save this as stereo profile and toggle it with 5ch HT profile depending upon the requirements)
4. Ditching the Audessey altogether by taking the front bypass option in Audessey dynamic EQ setting and taking custom EQ route for front speakers.
5. Disabling the center channel altogether and listening in the multi channel stereo mode ( since all his speakers are from Same model and brand, this could be a better option)
6. Upgrading the Stereo Source to a better CD player, DAC or streamer
7. Finally Upgrading to a better AVR with preouts ( instead buying an integrated amp above 100wpc is a better alternative anyday) Qacoustics will definitely benefit from more power in my experience.
8. Unpopular option is to upgrade to high quality front speaker cables
Hopefully this helps!