It should have at least 3 USB 3.1 busses. One for the top Thunderbolt ports. One for the Thunderbolt ports of the I/O card. Another for the USB type A ports (two on the I/O card and one internal). There could be USB for bluetooth? I would have to check a dump from ioreg to be sure. If you have GPUs with Thunderbolt ports then each pair of Thunderbolt ports will have its own USB 3.1 bus.
Double check my guess by plugging a USB 3.0 device into each port and using IORegistryExplorer.app (from Xcode tools) or run the following command after each connection:
ioreg -w0 | sed -E "/, id 0x.*/s///" | grep -i usb > usb_test1.txt
Give each test a different name to describe what port is being used.
Maybe repeat the test with a USB 2.0 device. Or do the tests with a USB 3.x hub which will count as a USB 3.x hub and a USB 2.0 hub.
You should be able to use any and all ports / busses. If you are testing USB Mass Storage devices, you can test multiple devices simultaneously using ATTO Disk Benchmark.app to see the max total bandwidth.
Two devices connected to a hub will be limited by the hub's upstream USB connection (9.7 Gbps for USB 3.1 gen 2, 4 Gbps for USB 3.0)
Two devices connected to different ports of a bus will be limited by the USB controller's upstream PCIe connection. A Thunderbolt host controller's upstream PCIe connection is 31.5 Gbps - a Thunderbolt peripheral controller's upstream PCIe connection is ≈23 Gbps so in either case more than one USB controller needs to be connected to reach the limit. You have to follow the PCIe connections through all PCIe bridges up to the CPU to see if there's any bottle necks. Slot 1, Slot 3, Pool A, and Pool B are four separate 126 Gbps connections to the CPU (all Thunderbolt devices are connected to Pool B - even those on GPUs in Slot 1 and Slot 2). There's also a 31.5 Gbps DMI connection for devices of the PCH (the type A USB ports and also USB 2.0 to the Thunderbolt controllers, T2 chip + NVMe, SATA storage).
https://www.apple.com/mac-pro/pdf/Mac_Pro_White_Paper_Aug_2021.pdf