Absolutely agree with you, the importance of the TO SHIFT is precisely described in the same chapter of the FCOM.
I don't think it's related to NAT, as I've seen it on flights to other European countries.
Nevertheless, as I stated before, TO Update is inhibited when GPS Primary is active, and even if it wasn't, what do you think the crew could be looking at when they call out the "runway update"? There's no indications to the pilot of this self-updating process of the FMS.
"‐ At takeoff, when the FM position is updated to the runway threshold position as stored in the database, possibly corrected by the takeoff shift entered on PERF TO page. ‐ In flight, the FM position approaches the radio position or the GPS position at a rate depending upon the aircraft altitude. Note: The FM position update at takeoff is inhibited when GPS PRIMARY is active."