As things stand TfL are correct. The only alternative route between Canary Wharf and Upper Holloway is via either Leytonstone or Forest Gate. The route has to be defined in the database before the system can charge it.
I suspect that when routeings were defined they put the whole of the Goblin in the same way, apart from Gospel Oak itself which is clearly obvious to go direct from Stratford.
Having looked at the map I can certainly see the benefit of allowing via Gospel Oak for Upper Holloway and possibly Crouch Hill as well. I suggest you write to email@example.com and request that they consider adding that route. You can point out that it avoids the need to walk between two stations at Leytonstone which should be seen as a benefit.