Setting XHCI mode to "Disabled" will do just that, disable USB 3.0 support across the board. All connected ports/devices will then operate at USB 2.0 standard regardless.
I must agree on the fact that the documentation provided regarding these settings (User Manual) is somewhat hard to understand. Gigabyte ought to invest in employing a native English speaker to write their English User manuals and BIOS descriptions instead of relying on the usual "Engrish" we see, that would help remove a lot of the confusion when it comes down to these settings.
The 2 USB 2.0 motherboard headers are shared with one of the onboard USB 3.0 headers, so having devices installed in those headers will steal bandwidth from your USB 3.0 ports and/or force them to run in USB 2.0 mode.
The Z87X-UD5H only supports USB 3.0 ports directly to the Intel chipset on one of the Internal USB 3.0 headers (Most likely the one labelled red on/off charge). ALL the remaining USB 3.0 functionality is provided by the 2x Renesas hubs present on the board, which also provide the additional USB 2.0 headers onboard, and possibly some of the back panel I/O USB 2.0/3.0 ports AFAIK.
Be aware, the Renesas chips are HUB CHIPS, as stated, and act much like any other standard USB hub. No drivers are required or available for these hub chips, and the Renesas drivers that are on the CD and the Gigabyte website are not for this board. Gigabyte tend to use one CD design for multiple boards, hence the reason you often get drivers bundled that are not applicable, something else they could improve upon.
Since some of the back panel USB 2.0 ports and the onboard headers, AND the back panel USB 3.0 ports are shared via the same hub and it's not really clear what is shared with what, it's extremely likely that if you have a lot of USB 2.0/1.1 devices, your going to run into bandwidth sharing issues with anything USB 3.0.
Add to this the convoluted modes present in the BIOS, and it's an even bigger mess.
Smart Auto, attempts to preserve the settings that were used in the previous boot, and assign those ports that are dual USB 3.0/2.0 (Probably Renesas hub provided ports) to the correct standard depending on the connected devices that were present on the last boot. That is the way I understand this.
Auto seems to check for devices and assign the switchable USB 2.0/3.0 mode to whatever it thinks is applicable during the CURRENT boot.
The remaining settings simply force the ports into the desired operating mode.
There is however a bigger issue. It seems that even on the 2x USB 3.0 ports that come direct from the chipset there is a high likelyhood of bandwidth / connectivity issues on this board. For example, I have an Akasa Baymaster, and the USB 3.0 Baymaster S. The Baymaster S suffers constant disconnect issues when a high speed transfer to an inserted 2.5" HDD is started. The older USB 2.0 Baymaster functions without issue, albeit at slower speeds. The built-in card reader is USB 2.0 in both models. Both motherboad USB 3.0 headers cause this issue. Being the only USB 3.0 device I have, I removed the Baymaster S and installed the USB 2.0 version in it's place. I've basically given up on USB 3.0 support on this board until Intel can provide some reliable USB 3.0 Drivers, and I can make some sense of what is shared with what.
