I think it's because when you use the BYPASS mode.. it does not use the subwoofer.. hence bypass. bypasses the video section and the subwoofer as I understand it.

I did too notice an increase in bass when using Stereo and Upsample. i prefer Bypass and Upsample the best for 2 channel listeing to music.
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Outlaw Audio 990 pre amp
Adire Audio sub (SVS 12.2 driver)
CAL Alpha tube DAC
Parasound P/HP-850 2 CH pre
Pioneer PL-530 TT
Polk Audio SDA 2B
NAD 2600A amp
Danger Boy here