I don't think it can be called an NR-only fare when it's clearly not an NR-only journey. It may be how the fare was derived in the back office, but TfL clearly list separate fare tables for NR-only journeys and for mixed-mode TfL and NR journeys - implying that the derivation of the fare might change at any point in the future.
But we're splitting hairs here...
... and while were splitting hairs
...
As you are suggesting, all of the journeys wholly on the London Overground are indeed configured for Oyster as TfL local fares, even when the actual price charged appears to be on the NR local tariff. In this way TfL is able to maintain its policy of not charging 5-10 year olds for travel on its services, for example.
The London Overground local journeys which appear to be on the NR local pricing structure are so priced to ensure that they are not undercut by longer journeys along the same corridor that are charged on the (sometimes cheaper) NR tariff. So, for example, Shoreditch High Street to New Cross (which would be priced at £2.80 adult peak on the normal TfL structure) is priced to be no more expensive than Shoreditch High Street to St. Johns (£2.40). In other words, the pricing is cheapest of the TfL local and NR local scales across all fare types. Shoreditch High Street to New Cross Gate, on the other hand, is priced at £2.80, presumably as there are no unfavourable comparisons to be made with Brockley which is also on the TfL scale.
Similar things occur elsewhere on the rail network where TfL fares apply. For example, London Liverpool Street to Tottenham Hale is priced at £3.10 adult peak (rather than £3.20 which is the normal TfL local fare).