Hi Daniel,
You’re pretty much spot on. The off-peak cap only starts being calculated after 0930 so initially you did cap at zones 1-2. If you’d realised that then you could have split at Stratford on the way home and saved £1.45. NR and NR-T do trump TfL-Ang which often creates anomalies, but you’re right, there is no standalone fare for 4-9 on NR because there are no NR stations in zone 9.
I’m sympathetic about the lack of progress towards back office calculations when discounted Oyster cards are involved. I don’t know why it’s taking so long, I can only assume that it’s not seen as a priority. The ability to link railcards to either contactless cards or a dumb Oyster style card is part of the second phase of the current rollout of PAYG to areas of the Southeast. It’s not likely to happen before 2024 at the earliest though.