Hi Adam,
Out of interest, what fare did they refund you down to?
The simple answer is that anyone using that route will be overcharged because it’s not defined in the fare database. There are two avoiding zone 1 routes defined. Both of those entail going through zone 2. I agree that an avoiding zones 1 and 2 fare is entirely reasonable using that route, but TfL will need to get sign off from National Rail before they can impliment it. I’d definitely write/email to them asking them to consider adding such a route for Central line to Great Northern destinations.