The line between Moorgate and Highbury & Islington is surely charged at the TfL-LU fare (same as Forest Hill – Highbury & Islington) and thus doesn’t invoke the NR-only fare? ie if you touch the pink reader at H&I it would be the same as Canada Water or Whitechapel (and presumably if you use the OSI at Shadwell?).
The NR-only fare seems like change at London Bridge onto Thameslink, change at Farringdon and arrive at Moorgate (with Farringdon – Moorgate possibly still having a residual NR route for fares even though the line closed) and leave via Liverpool Street gatelines.