Hi JR,
The Elizabeth line core is actually defined as Paddington to Stratford/Abbey Wood. However, there are a number of issues which determine whether the mixed mode will apply to parts of the core.
Taking the Canary Wharf example first. Oakleigh Park to Abbey Wood is historically defined as NR only taking Oakleigh Park to Highbury & Islington to New Cross to Abbey Wood. This was actually a success of this site back in the day. Today you are likely to use the EL from Moorgate/Liverpool Street, but you don’t have to and they can’t tell if you have, so NR fares still apply. It’s likely that they decided that intermediate stations between Liverpool Street and Abbey Wood should also have just NR fares to avoid the situation where travelling further on the same train costs less.
As for Stratford, I’m puzzled. That can also be done only on NR by walking along the EL platforms to Liverpool Street and using a Greater Anglia train. It might be worth asking TfL whether they agree that this counts as an option avoiding any of the EL core. You could also make the journey changing at Highbury & Islington and avoid zone 1 altogether, thus getting an even cheaper fare.