Just to emphasize, I don’t think I can be much help at this point, but I do see this which sticks out (several times):
[ 3.624112] tegra-pcie 10003000.pcie-controller: link 2 down, retrying
[ 3.626162] tegra-pcie 10003000.pcie-controller: link 2 down, ignoring
Followed later by:
[ 10.555032] pci 0000:01:00.0: xHCI HW not ready after 5 sec (HC bug?) status = 0x801
I don’t know what device tree entry might be related to that, but it seems like it was trying to bring the link up. Most of the custom carrier board cases where something just does not come up, but should otherwise be ok, fall into the device category of failure.
The lspci won’t show something if the link is down. The bridge and the USB controller which shows up have no errors, so I would expect that if the device tree were correct, then your other device would also show up. Someone else will need to look at the device tree since I have not worked on custom carrier boards.