I confirm both lines are active low, and mapped to gpio5/6.
Also, there is a pullup resistor connected to each line.
Firmware programs both gpios as input, and the pullups effectively enable both WiFi and PCIe at reset.
How did you check the direction and value of the gpios?
I tried a couple of experiments last night and it looks like the firmware does program this as inputs with value 1. Previously, I was checking the value after making gpio5/6 outputs and this showed the value as 0.So it looks like the defaults are fine. It still doesn't explain why 2 of us are having the same issue with a certain type of pci card. I will try resolving that separately.