I think the biggest advantages of a built-in filter is being there all the time while the advantage of an add-on filter system is allowing different filters to be used.

So you can think in the built-in ND as an "extra" filter that you can use without the filter adapter for simpler situations (where the 3 stops would be enough). And then use the external filters for more sophisticated setups. For example:

• You could use a second ND filter with more stops, allowing you to reduce even more the light entering the camera. Using a "big stopper" with 9 stops plus your internal with 3 stops, gives you a quite dark setup for long exposures during daylight.

• You could use a polarizer together with the internal ND, so you could make a long exposure of water on a river without some of the reflections and making the leaves around it more "alive".

• You could use a graduated ND filter together with the non graduated internal one, making it possible to reduce light differently in separated parts of the scene.

Just notice though that the quality of the internal and external filters can make a lot of difference in the final image quality. And if you happen to have a better external filter just use it instead of the build-in.