It's been my experience that the "Disk Not Ejected Properly" issue is not a USB 3.0 issue but an electrical issue with the USB 3.0 device. I have had the issue with my 5,1 Mac Pro with both the KT4004 and the 1144C cards when I was using it with a Micronet Fantom HDD. When I switched to an Hornettek Viper USB 3.0 enclosure with a fast Seagate HDD, the problem went away. Also, the Fantom drive could make up it's mind if it was a USB 3.0 or a USB 2.0 Device. The description would change in "System Information."
Also, I have an MBA with native USB 3.0. I use an Orico 2.5" USB 3.0 enclosure with a 2.5" Hybrid SHDD. I only use that drive occasionally, but it has the same "Disk Not Ejected Properly" issue.