@CaseySJ
Something I noticed for awhile is that I no longer have XHC5 or SSP1/2 and haven't for awhile. Seeing recent posts only made it more obvious something is off. I have done a clean install of Big Sur but it was like this on Catalina as well. I do not have a flashed TB controller or any TB add-in cards.
I have XHC and AppleUSBXHCITR. I use an LG UltraFine 5K and that adds a second AppleUSBXHCITR. To rule out differences in my tweaked EFI and yours as well as the LG UltraFine, I have booted with your EFI from OC 0.6.3 and disconnected the LG Ultrafine and used a DP monitor.
I still don't have XHC5 or SSP1/2. The single AppleUSBXHCITR should be XHC5 as it used to be. I've attached a copy of my IOReg. Additionally, if I use Hackintool to generate a USBPorts.kext, it wants to rename AppleUSBXHCITR to XHC, giving me 2 XHC in Hackintool, and it uses ports SS03/04 which are duplicate names.
This is with your OC 0.6.3 with the only change being SMBIOS.