Yes, it does. Quite a lot actually.
If you select the JRiver Media Center option, all Windows applications will play through MC via the WDM Driver, which is an input to MC. Media Center must be running for that to work. Depending on what you are playing from in Windows, you may be able to send audio to the WDM Driver in Exclusive Mode, which would mean that Windows won't remix the audio before passing it to MC. Other applications can only output in Shared Mode. Chrome, for example, will only play in Shared Mode, which means Windows will remix the audio and combine sounds from multiple sources before passing it to MC.
If you select your DAC, all Windows audio will play directly to your DAC, and it would likely use Windows Direct Sound which will remix the sound to combine audio from all sources and output them to the DAC. This will result in lower audio quality. If MC is running and playing to your DAC in Exclusive Mode, Windows will not be able to play system sounds. Those sounds will be "lost".
So which output device you send Windows sound to depends on whether you want sounds external to MC to be played through MC, or want sound to be available at all times even if Media Center isn't running.
Inside MC, you must select your DAC as the Audio Output Device. Use Exclusive Mode, and WASAPI or ASIO for best audio. All audio from MC will then be played directly to your DAC using the settings in MC.