I'll send you the executable. I can give you the source code as well if you wish so you don't need to reinvent the calculations in case you want to try some of it inside the game.
You can perhaps put something like this as some sort of experimental alternative control scheme into a test build, and see how people react. Maybe it'll be bad for your typical player, I don't know, but as I played with it, I realized I can more easily "do what I intended" than with what you currently have in the game. There's no flipping whatsoever if you keep orbiting inside one hemisphere (front or back)
There's a particularly satisfying (and I'd guess useful) 180 turn maneuver where you yaw or pitch to one side and at the same time orbit the camera to other side to compensate. Try it out.
The main problem with craft-centric yaw/pitch/roll control, except that is exceptionally nerdy ;), is that it's meaningful only if the camera basis is aligned with craft basis, or at least very close in alignment, so that player's mental model of directions corresponds to what they see . In other words, it's for first person or close-behind third person view. As soon as this alignment goes out of whack, the confusion sets in and it becomes very taxing for player to mentally map controls to what they see. It's especially incompatible with free orbiting camera, as the relation between craft and view bases changes from moment to moment. The player constantly needs to look at the graphic of the craft, figure out its alignment on all 3 axes, and mentally re-map the controls to get where they want in the world.
The new controls are better but I still wouldn't call them "intuitive", especially for more casual players who don't have affinity for "realistic" piloting. I'll play some more and report back.
Imo the best way to think about control scheme is to take into consideration what the player needs to do in a typical gameplay loop, and asses which control scheme best caters to it. With classic 6DOF I think you confine the player to the (near) first person view if they want to maneuver without frustration, so they lose the joy of observing what their craft and enemies are doing from various angles while still being able to successfully steer at the same time.