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Shoreditch High Street is a new station on the extended East London line and I can confirm that for fares purposes the station will be classed as a Zone 1 station.”
This means that using the line, as was initially though, as away to divert traffic away from the crowded lines in Zone 1 to provide relief on the Underground is now less of an incentive. The old Shoreditch station on the East London Line was in Zone 2 and it was thought that the whole line from Highbury & Islington to Brockley/New Cross should be inside Zone 2.
In fact the 2010 Tube map that TfL released in November 2006 showed the entire Overground network include the second phase of the East London Line Extension (ELLX) to Clapham Junction. This clearly showed that to travel from Clapham Junction all the way round to Highbury & Islington would have kept you in Zone 2, therefore giving you a cheap ticket to cross London without using Zone 1.
As well as increasing fares for TfL to gain there is also the fact this simplifies Oyster usage as the system doesn't have to work out which way you went as now a cross London journey using the ELLX means a Zone 1 trip.
The re-zoning of Shoreditch High Street also means there is potential now for the system to charge wrong for journeys made with Oyster as Clapham Junction to Highbury & Islington is still possible using only Zone 2 if you go via Willesden Junction and use the West London and North London Lines. Whether or not there is enough of an incentive to do this when you could use a single train remains to be seen.
What has been said about the zoning of this station is that it was a condition laid down my the DfT for funding of the ELLX phase 2 from Surrey Quays to Clapham Junction, which if true could be a good reason why TfL accepted it to allow the South London Lines adding to the Overground network. So in the end there is worthwhile benefits to this.