Yes I think I’m using config #1. Here are some messages from dmesg which probably confirms that -
dmesg | grep pci
[ 0.140887] node /plugin-manager/fragment-500-e3325-pcie match with board >=3489-0000-200
[ 0.140904] node /plugin-manager/fragment-500-e3325-pcie match with odm-data enable-pcie-on-uphy-lane0
[ 0.257273] GPIO line 459 (pcie-lane2-mux) hogged as output/low
[ 0.260531] iommu: Adding device 10003000.pcie-controller to group 50
[ 7.538466] tegra-pcie 10003000.pcie-controller: 4x1, 1x1 configuration
[ 7.550173] tegra-pcie 10003000.pcie-controller: PCIE: Enable power rails
[ 7.559428] tegra-pcie 10003000.pcie-controller: probing port 0, using 4 lanes
[ 7.561610] tegra-pcie 10003000.pcie-controller: probing port 2, using 1 lanes
Let me know if I can check something else to confirm the config #1 state.
Currently, I can access my pcie device and after making the above change to enable ‘usb3-std-A-port2’ in device tree, I can use usb ports too (both the micro usb port and USB A port on the devkit board).
I understand from looking at the platform adaptation doc that in Config #1, usb3 port will not be enabled. But in my case once I enabled config #1, I was not able to use any usb port and the above change to device tree helped. So not sure either what is going on.