Hi,
I would expect that MQA stipulated that their decoding can only provide stereo output, and any DSP function following decoding cannot be used - such as a subwoofer.
Some subwoofers allow the amplifier speaker output to be connected to them, but for non-MQA source material, the subwoofer line input is now competing with the connected amplifier stereo speaker output.
Regards,
Shadders.