NR only does what it says on the tin, it only provides a discount on journeys priced on one of the NR or Overground fare scales (the Overground is part of National Rail, even though TfL don't want to publicly admit it).
There is no discount at all on "mixed mode" journeys, or ones priced on the LU/DLR scale.
So it can sometimes be cheaper to "split" by using an NR only discounted Oyster card for the NR portion of the journey, and then a separate undiscounted Oyster card (or contactless card/device) for the LU/DLR portion of the journey.
Otherwise the problem is that the OSI joins up the two "journeys" into one, despite this being more expensive than charging them separately. It's just one of those Oyster quirks.
Alternatively a paper ticket to somewhere with LU validity (e.g. the opposite side of London) can sometimes also be cheaper than the above split, but it depends on the exact journey you're making.