The plugin has to be bypassed every time you are exporting audio from your DAW. Otherwise, the correction will be applied to your master bus mixdown. It is important to understand that the plugin is meant to calibrate your individual monitoring setup ONLY, not others (just like acoustic treatment would need to be different for different rooms). Failing to bypass the effect would mean adding the sonic anomalies of your system to the rendered audio.
Hard-bypass the plugin for rendering your project
Make sure you make a full plugin bypass in your DAW, not just disabling the calibration inside the SoundID Reference plugin, but fully turning off the plugin in the channel plugin insert strip of your DAW.
We have also introduced a render bypass notification system that currently works on selected DAWs.
You can read more about it here.