just test it
i can only answer for vag me7.5 1.8t and if the ecu enters bootmode it wont power up normally. all the other pins are basically unused while you are benching it.
In vag cars you have k-line from the obd2 port all the way into the ecu. communication is not a problem.
when you are done writing the ecu in bootmode and cycle the ignition all of the dtcs will clear on their own (if there are any).
I never had a problem with the cluster complaining about the immo after i wrote the ecu in bootmode.
just try it and you will know
