Hi Daniel,
I think you’ve hit the nail on the head. It will be an unexpected consequence of the fares freeze which wasn’t allowed to include Underground set fares. The lines out of Liverpool Street, especially beyond zone 6, have additional considerations as part of the deal to allow TfL to take over those services from Greater Anglia.
We’re still under 2 months from the fares revision, so it’s possible that no-one has yet noticed. I’d imagine that most people on Underground set fares are resigned to the fact that the fares freeze doesn’t apply to them. I’m a little surprised that MPs in affected constituencies haven’t kicked up more of a fuss, but perhaps they just don’t realise.