Does motherboard audio processing affects its USB outputs (to external DAC)?

It probably doesn't affect the external dac since the effects are applied on the integrated soundcard of the motherboard, but the audio signal is only processed by the dac. Anyway you can easily disable those enhancements by going into the sound section of the windows control panel and selecting the properties of the proper output device.

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The answer to your question is maybe. It really depends on the audio player software you use and the audio drivers the software can use. For example, the Qobuz or Foobar (or JRiver) app can use WASAPI or ASIO as output. WASAPI and ASIO bypass all of the Windows Sound mixer and are able to achieve bit perfect playback. There are other player softwares that can use these drivers. You generally have to go to the settings of the program and choose the output. Programs like Windows Media Player or Windows My Music are unable to use WASAPI or ASIO and their sound goes through the Windows mixer and thus the sound is subject to all the foibles and distortion of the Windows mixer. FWIW, I won't use Amazon HD Music because its so called app doesn't allow you to use WASAPI to bypass the Windows sound mixer. I probably didn't explain this very well but someone with more knowledge will explain it better.