Concerning: 04:00.0 USB controller: Renesas Technology Corp. uPD720202 USB 3.0 Host Controller (rev 02) (prog-if 30 [XHCI]) Flags: bus master, fast devsel, latency 0, IRQ 19 Memory at fe6fe000 (64-bit, non-prefetchable) [size=8K] Capabilities: <access denied> Kernel driver in use: xhci_hcd Kernel modules: xhci_pci Although xhci_pci is loaded, lsusb does not show any Linux Foundation 3.0 root hub. Device is detected and works properly, when computer is booted with 6.11.0.
Is this lspci output from the working 6.11 system? On 6.12 you should see Kernel driver in use: xhci-pci-renesas Kernel modules: xhci_pci, xhci_pci_renesas and you need CONFIG_USB_XHCI_PCI_RENESAS to have this module if you are building your own kernel, see commit 25f51b76f90f.
Please bisect: https://docs.kernel.org/admin-guide/bug-bisect.html
CONFIG_USB_XHCI_PCI_RENESAS and loading this module make it work. This option and module weren't required in 5.x.