It's a factor of both, even though that's a cop-out answer..
Last year's Spurs team finished 9th defensively, 6th the year before, and 3rd the year before..
This is impressive when you consider the rotation players the Spurs have been putting on the court in those years..terrible defenders(Finley, Mason), soft defenders(Bonner, Jefferson, Parker), average defenders as stoppers(Jefferson, Hill, Bogans, Udoka) and overall poor defenders(Blair)..all those guys were serious rotation players during the last few seasons..
The fact that the Spurs have been putting out players like that, and the fact that the Spurs' have had almost no length or athleticism, yet they still finish high in defensive rankings, means Pop's system still works well..
The Duncan-Bowen factor is obviously the difference in the Spurs being an above average/good defensive team to an elite team..Bowen is a top 2 perimeter defender of his generation, and Duncan is one of the best anchors of all-time..
Bowen's loss has been felt most in 1 on 1/isolation defense..last year's Spurs team was 27th in the NBA at defending 1 on 1/isolation plays, absolutely horrible for a playoff contender with high hopes..it is also felt in defending screens, where the Spurs ranked 18th..Bowen was always one of the best in the NBA at running around and fighting through the screen..