I am checking some fares from Winchmore Hill (Great Northern, Zone 4) to Custom House (Elizabeth line, Zone 3) and Royal Albert (DLR, Zone 3), passing through Central London.
To my surprise, the fare to Custom House (Elizabeth line) is cheaper than the latter, with the difference being an additional DLR leg at the end. The presence of the DLR leg, but not the Elizabeth line between Liverpool Street and Custom House, attracts the premium.
I am also checking some fares from the south east to Liverpool Street (Underground) and they also don’t attract a premium as well. Therefore I believe that the Elizabeth line mixed mode premium only applies to the section between Paddington and Liverpool Street, while the section between Liverpool Street and Abbey Wood is dual-scaled. (In addition, the Metropolitan line between Farringdon and Moorgate is also dual-scaled as well which needs to be corrected in the fare guide. Travelling between an NR-only route and Barbican does not cause a premium).