From my brief googling I think the programming is for the immobiliser. Your key has a transponder and if you swap out the ecu they won’t match any more.
I see a few eBay listings people selling the ecu and the transponder chip so you don’t need reprogramming.
I’ve a little experience with remaps on Smart cars and with them the ecu is coded to the keys, so you need to programme a key when you swap an ecu.
Looking forward to your findings.