I'm not all that familiar with Nikon's 3D focus...does that have to do focus points/area or tracking a subject or both.
Typically, there are the AF points (manually choosing or letting the camera choose) and the focus mode...which are separate things.
I believe that choosing a specific focus point (or area, on some cameras) is the way to go. If you let the camera choose the focus point for you, it may not choose what it you want it to.
As for the focus mode, there are two basic modes; still subject or moving subject. (AF-S & AF-C on a Nikon). In still subject mode, once the focus is reached, it stops and locks the focus. It also won't take the shot until it has achieved focus. In moving subject mode, it constantly re-focuses and lets you snap the shot at any time. Both can work well if you know how to use them and are comfortable with them.
Most cameras will have a hybrid mode that locks the focus like still subject mode, but will try to track the subject & refocus if it thinks the subject is moving.
And some cameras have some more complicated features that I'm not too familiar with....so RTM.
One thing that would influence my decision in this case, is that (with Canon cameras at least) the AF assist light only works when in still subject mode.