Well, what do you know!
Got a letter in the post this morning, where they 'looked at the case in greater detail' and decided to give me rail vouchers for £2.60 as a goodwill gesture.
Thus, GA is clearly not admitting its mistake, or acknowledging the fact that it can't make people pay more, and will presumably continue to do nothing to resolve the problem happening again during future engineering works.
Hmph. The engineering works are still ongoing and I bet a lot of people are therefore overpaying. I wonder if it'd be worth you phoning up the Oyster helpline not to request a refund, but just to complain to them about GA's attitude in the hope that perhaps TfL can have a word with GA about how to use the Oyster system properly.