Hi Jack,
It’s complicated.
You might get a bit of a clue reading the Fares Guide page, but the anomaly you are referring to is niche. Firstly, Amersham to Finchley Road is on the standard TfL-LU scale which is usually the cheapest. Although Epsom is in zone 9 its fares are set by South Western Railway so they don’t quite match the NR scale. Brentwood is on the TfL-Ang scale which is a hybrid scale forced on TfL when they took over the Anglia services out of Liverpool Street. It used to be worse, but now the differences between TfL-LU and TfL-Ang are limited to zones 7-9 and longer distance off-peak journeys in zones 2-6.
So, initially there were three scales covering just about everything on Oyster. TfL-LU was the Underground, DLR and any NR company using TfL’s fares (obviously including Overground, but also C2C and GWR amongst others). NR was for the late adopting companies (Southeastern, Southern etc) and also applied to any wholly NR journeys using Overground, C2C etc as well as late adopting NR. Finally NR-T was any journey on late adopting NR which also included Underground or DLR. There are some variations, but that’s broadly the picture.
After some complaints around discontinuing season tickets when LO took over some of Southern’s services, The DfT imposed restrictions when they took over the Anglia routes. These hybrid fares were to apply on any TfL journey that included the Anglia routes. However, where a journey included TfL-Ang, TfL-LU and late adopting NR it became, I think, too complicated. The result is that NR overrode TfL-Ang and produces the anomaly you have discovered.
There is no point in asking TfL to reduce fares from Brentwood to Whitechapel because they can’t. If you highlight the discrepancy when you include late adopting NR routes the outcome will either be nothing, or the lower fares will get raised. I hope this helps.