As I mentioned upthread, I did write to XC about this, to get their view on whether Advance tickets could be excessed by the issuing ticket office. They have come back with a well written response, which I reproduce below.
"I do appreciate you providing a copy of all your son's tickets for the journey in question, as this has helped with our enquiries into the issue you've raised. Having discussed this in depth with our Pricing & Revenue Manager, he has confirmed that it is indeed valid to change Standard to First Class on Advance tickets by means of issuing an excess; in circumstances such as this, it would usually be the case that the incorrectly-issued Standard tickets would be withdrawn, and full First Advance tickets issued in their place instead, but the issuing of an excess is still valid as long as this is done at a station prior to travel.
It would appear that the confusion here has apparently arisen from the fact that it isn't possible to issue such an excess fare onboard a train if the customer had the opportunity to do this beforehand; in such cases, a full First Class single fare for the journey in question would have to be charged instead. As the issuing of a Standard-to-First Advance excess isn't as common as withdrawing and reissuing the tickets in their entirety, this would seem to account for the Train Manager's belief that your son's tickets hadn't been validly issued by the staff at Berwick station, which is deeply regrettable.
As the reservation coupons have allowed us to identify which service you son travelled on, I've personally shared your feedback with the relevant Customer Service Manager responsible for the Train Manager in question, in order to ensure that he can brief her about this particular matter, to ensure that similar errors don't happen in future; I'll also make sure that our Customer Relations Manager is made aware of the incorrect information having been given by one of the team, so that action can be taken to address this going forward. In the meantime, I'd like to offer my heartfelt apologies for the problems your son faced when he travelled.
Thank you for taking the time to bring this to our attention; I do hope we'll be able to welcome your son back aboard soon."
So yes, everyone here was right
Again, thank you to everyone who took the trouble to respond to my initial enquiry.