It's not so much a difference in SQ, if that's what you're asking - these only ensure that you can actually run DACs. Some mobos don't output 5v in some ports especially when you have a lot of devices plugged in via USB - recall all those "my DAC doesn't work and I don't know why?" posts with "did you try all USB ports in your computer?" replies. These will just guarantee that you can have a keyboard, mouse and gamepad (in their dedicated "gaming peripheral ports) plugged in along with an external HDD, a mobile device (being synced+charged) like a tablet and a smartphone, and of course the DAC all plugged in simultaneously.
Yes, I was referring to SQ.
Based on your explanation, these USB ports for DACs might actually solve a problem I've been having for a while now. It seems like the USB ports in my current board sometimes degrades the SQ of my DAC where I have to unplug and replug the DAC into another port to restore the SQ to where it originally was. I do have a lot of external drives plugged in along with the DAC so I guess that might have something to do with it.
However, when you think about how many of the mobos that have this feature tend to be red motherboards which in turn tend to have the virtual surround hardware and in some cases also a dedicated headphone output stage, then how likely would you really use a DAC with those? Plus the red boards are usually only a few bucks more than the blue boards. Even if you want to play games with a headphone that needs a lot more clean power, if you still want to utilize surround sound, you'd have to use SPDIF and not USB so you can use the built-in DSP chip in the mobo.
I use the built-in audio outputs of my motherboard exclusively for my 5.1 surround computer speakers which I use for gaming and videos. I prefer having a dedicated 2-channel for music only DAC hooked up to my loudspeaker system and also for my HPs and IEMs.