But it is shown on the schematics, I guess?
It is on the schematic on page 10 of the manual. The schematic seems accurate from what I can tell, but there is no other mention of this port beyond that.
What's probably confusing people about the USB 2.0 port is that generally it is expected to have a USB *header* to connect to front panel USB ports or such (like with the USB 3.0 header), instead of a literal USB port sticking out of the board. The reason for that port existing seems to be that the GL825 USB 2.0 hub can support 4 ports, and the Blackbird design has one spare. If you look at the schematic, on the left side is the GL825 hub. It is connected to the CM6206LX audio device, the front panel (I'm unsure why the front panel ports are connected to both the TI USB 3.0 controller and the GL825 hub - maybe it is for if a USB 2.0 device is plugged into them?), and the spare port.
IIRC, the front panel connectors always carry 2 ports and not 1, which might be why it is a literal USB port in this case. I might be wrong about that, though.
Since the internal USB2.0 header is not detailed anywhere in the manual, does anybody know if there are security or other implications to using this port? For example, if flash storage were attached, it is still behind IOMMU? Does it still connect to the same Texas Instruments USB host controller?
The USB 2.0 port eventually connects back to the TI controller through the GL825 hub. I thought USB didn't have DMA like PCIE and such do, so I'm not sure if the IOMMU has a role here. A *controller* connected over PCIE would interact with the IOMMU, but the GL825 only connects over USB to the TI controller so that isn't an issue here. If anyone that knows more wants to correct me please do, but I don't think there are any additional security concerns with this port compared to the other ports.
Slightly off topic, but one idea I thought of was to make a little USB 2.0 hub expansion board connected to a PCIE bracket for the back of the computer, connected to the lone USB 2.0 port with a USB cable. It wouldn't do anything for USB bandwidth, but would give more USB ports for peripherals and such on the back. There are only 2 ports there now, so having more would bring it more in line with x86 boards.