Hi TomKure, have you ever measured (or just compared by ear) those special motherboard USB ports with regular ones?
Yes, I have measured and listened to Modi+Magni stack through 4 kinds of different USB ports. The strange thing about Modi was that when playing pure sines with frequency between 20 and 200 Hz, I could hear a strange noise in the sound.
The noise was the loudest when I still had my old motherboad, a Gigabyte EP45-UD3 and used the regular USB2.0 ports in the back. Also, the Modi measured the worst from those. The best measurements and least audible noise in the sine test signal, I achieved when connecting the Modi to my laptop or to the designated DAC USB ports on my current motherboard. I also tested my current motherboard's USB3.0 ports, which were somewhere in-between, but closer to the old mobo's USB2.0 ports (the old mobo had only one kind of USB ports - plain USB2.0).
I also measured my EMU0404 USB from the following USB ports: old mobo USB2.0, new mobo USB3.0, new mobo USB2.0 DAC ports. Differences were next to none, yet there were some, confirming the DAC ports were the best.
To summarize, I would sort the ports as follows, based on both listening and measurements, from worst to best: GA-EP45-UD3 USB 2.0 < GA-Z97X-Gaming GT USB plain USB 3.0 < Laptop (Acer Aspire 5738G) USB 2.0 = GA-Z97X-Gaming GT DAC USB 2.0.
When listening to music however, I doubt I could tell them apart, maybe only with the noise-sensitive Modi, and only by hearing/not hearing very quiet noise during silent parts of tracks, which happened with my old mobo. Not with the new one using the DAC ports.