There is a post discussing a wake problem related to CAN_WAKE signal, and NVIDIA said in the last post that the wake from sleep using CAN_WAKE is not supported.
Yes, CAN wake as a GPIO pin is supported on TX2.
Can you check what is the pin configuration?
Read these registers:
Pinmux: 0x0c303048
GPIO: 0x0c2f1c80
you can use devmem tool to read these registers from linux userspace.
Let me know what value these are configured to?
This pin should be input from gpio and pinmux.
Also, make sure you are toggling on Pin1 of Expansion header.