Hello,
The User Interfaces for capture was designed around the expectation of using non-3D cameras. You may be able to adjust the code/configuration a bit to have it work. Although you'll also need to make sure that gphoto2 supports your particular camera.
That being said, with a single 3D camera the need for the capture UI is diminished and you can just use the camera directly. There was some testing done with the Fuji W3 in this fashion, with good results.
When you run through calibration and dewarping, just make sure to follow the specified naming conventions.
Hope that helps, and please let us know how things go.
Thanks
Justin