I would run the clutch wire to EWS to do the swap correctly.
This describes the wiring changes needed when swapping a manual transmission into an E46 that originally had an automatic transmission. Remove EGS First step is to remove the transmission control module (EGS), located in the electronics box near the brake master cylinder. Connector A7000...
I'm sorry, but that is correct only for US and JPN version of the car. Clutch switch is NOT connected to EWS in European version cars. You can check that in TIS. I can also confirm, that clutch switch connector pin 4 is unpopulated in harnesses I took from local (German market) cars.
Also, the configuration rules for EWS default coding in NCS Expert says that P/N/clutch starting condition option is set only for US, JPN or AUTO option.
So the correct swap is:
a) US and JPN version: Connect clutch switch to EWS, no reason to code the EWS
b) other versions: Not to connect clutch switch to EWS, need to code the EWS
Also, is there any need to code default settings in all control units in the car? Most units have no option based on auto/manual option. I know only about instrument cluster and EWS.