Why does SoundID Reference lower my output volume?

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Safe Headroom

By default, the output is lowered when the Safe Headroom feature is enabled. SoundID Reference cuts and boosts certain frequencies to compensate for the inconsistencies in a particular output's frequency response. Boosting certain frequencies creates a risk that the digital audio will peak above 0 dB and clip. The Safe Headroom feature lowers the output volume by the maximum peak in the correction curve to prevent the output from clipping (prevents gain-staging related audio distortion).  

You can disable it at the risk of introducing clipping by turning off the Safe Headroom feature and turning the volume fader all the way up.