Can't we build our own presets? We are constantly dealing with custom rigs of various configurations.

Sure! Just align the cameras the best you can, trying to input focal length and lens distortion as accurately as possible. Not to the shot you're particularly using to create the preset but to the characteristics of the rig you're using. I usually use PTGui or Huging for getting the focal length and distortion, then input manually the Yaw, Pitch and Roll parameters for each camera in MistikaVR, trying to keep them as square as posible. Then you can just right click on the "Clips Stack" window and "Save Preset" Don't Improve alignment neither Match Color for creating the preset, you can do that whenever you have to use the preset.