It's badly written, it should say "Pay as you go fares for some journeys on London Overground and TfL Rail routes that operate to and from Liverpool Street, will change."
If you look at this document from 2015 regarding the transfer of Greater Anglia services it says that "The terms of transfer of the services require TfL to ensure that fares are set in such a manner as to not create new anomalies in the overall national rail pricing structure (see further details in Appendix B)."
https://www.london.gov.uk/sites/default/files/gla_migrate_files_destination/Appendix 1 2015 May fares revision paper advice to Mayor PDF.pdf
It's probably a legacy thing. Before Oyster Pay As You Go was accepted on all National Rail services all fares were charged at the same farescale, as it was usually only available on routes with joint availability and thus charging the same rate as LU made sense. Great Western made a decision to accept PAYG on its line from Paddington before the rest of National Rail and hence it is charged at the TfL farescale (obviously not relevant really except on the Greenford branch now that TfL Rail has taken over). I think the only route from the pre-Oyster on National Rail that charges NR fares is Southern from Balham.