Hi there,
I don’t know the Answer but AGREE on building with the CONF_GPIO_SYSFS flag
also I’m thinking with the JetPack flash You should still be able to use the gpiodev
I’m pretty sure I have seen this b4, Not sure if they reflashed or found the iopins but your in the right neighborhood. Maybe one of the SEEED ninja’s 
can chime in?
HTH
GL 
PJ