BINGO!
I never could get the serial to function, so I improvised. I actually edited the mactab file to point wan0 at the silicom and lan0 at the integrated nic (mgmnt), this way I could still SSH into it on the network. After that, I ran the echo off script to verify I could disable the bypass, it did... then I ran the other script to add it to wanos for automatically shutting it off. I restarted (sudo reboot) and it stayed in bypass off. Then I added the other MAC on the silicom as lan0, restarted (sudo reboot) and it stayed in bypass off... However, after powering it down (sudo poweroff) and restarting it, it is in bypass again.