Z-Buffer 3D does not create fully natural Stereo 3D by design, instead it’s a lot faster. It’s usually dialed in to provide a pleasent (even stronger than with Geometry 3D) 3D-effect in the distance, but has ‘weaker’ 3D for nearby objects. Geometry 3D for Fallout 4 will be available with the next vorpX update.
Just be aware that both methods each have one advantage and one drawback. While G3D provides the more natural 3D, Z3D is roughly twice as fast. High framerates are as important in VR as Stereo 3D.
In case of Fallout 4 that means that G3D will not allow you to achieve a VR compatible frame rate in many situations unless you own an extremely fast PC (fastest Core i7, GTX980Ti). You’ll be able to decide yourself soon.