I can (partially) reply to myself as I found some more info, in hope it will help someone down the line.
Basically software like Thetis expects to be able to talk to HL2 IO board via i2c. If it can't it will flip (despite setting the no IO board in setup.
So one has to include this i2c functionality in the firmware. There are some ready made firmware routines in the github repo, hut they are all in C. So anyone who prefers python is out of luck.
Anyway, I created a new version of n2adr_basic folder. I removed all the stuff I don't need from the main function (icon ah 4, voltage/band decode etc). I added a line to set REG_RF_INPUTS to zero (can be changed via i2c later).
Also I modified the IrqRxTxChange function in the n2adr_lib/i2x_slave_handler.c file to drive Out 1 high on TX. That's my only change.
Hopefully it will restore Thetis functionality.
73, Łukasz