Can USB 3.1 enabled at Uphy #4?
No, please refer to lane mapping in OEM DG, UPHY4 is configured as PCIe.
Based on the document “Jetson_AGX_Devkit_Pinmux_Configuration_Template_v1.03.xlsm”, it could be changed to USB3.0, but as you mentioned, it only support PCIe, is there any mistake for the document?
No, the document has no mistake.
The AGX hardware has capability to change between PCIe and USB, but we only support customer to use the same configuration as our devkit.
If you really need to use those configuration, please contact NV sales to highlight your issue.