3D and VR are very different animals.
There are certain design elements, especially how the UI operates, that need to be taken into account with VR that you don't with just 3D. Elite: Dangerous made the decision to include those elements from day one. It's why mouse players have this "The galaxy map doesn't work!" moment when they star to play VR, but HOTAS players, who bound their galaxy map controls to work with HOTAS, don't. From hooks for controls, to HUD layout, to the design of the cockpits themselves, Frontier Developments designed this game from day one with VR in mind, and it shows, because this game is brilliant in VR.
Cloud Imperium Games seem to think this sort of thing be patched in at a later date, but they've already made way too many design decisions that a lot of people believe will make a poor VR experience. From HUD layout, to cockpit design, to some controls, and especially the way the game seizes control over your avatar's movements, it's not really designed with VR in mind.
Its kind of the way a certain online Mechwarrior game made an early decision that it should be a First Person Shooter with 'mechs, and not a battlemech simulator. You can try to set up your HOTAS to emulate a mouse, but it will always be a subpar experience, simply because a joystick is not a mouse. It may still be a good experience, especially in a single player game against AI, but you would get better results with the controller the game was designed to use.