This is due another un-fixed bug of CloD, the human player occupying 2 positions simultaneous (easy to see in MP roster).
In two* crew planes when the human pilot goes for gunner/bombardier/observer position and then return back for pilot position the AI don't assume the observer (gunner, etc) position back.
Workaround: Instead use the command "Manned Position #1" or 'Changed Manned Position" (sequentially) to return to pilot cockpit use the command "External View" - that lead to another un-fixed (but easy to fix with Notepad) CloD bug:
Are two commands with "External View" name, use the first (default keys is
Alt+F2) (View category commands).
Now the plane are under control of AI, in all crew positions.
Then use the command "Take Control of Selected AI Aircraft" to regain control of your plane.
More "realistic" way to change positions impossible.
It's CloD!" * The issue affect BF 110, Ju-87 Stuka and now Beaufighter.
In more than 2 crew planes (Blenheim, He 111, Ju 88, Br.20) this "jugglery" can be avoided returning for pilot position through bombardier position:
Gunner > Bombardier > Pilot.
As the AI Bombardier do nothing, no issue in player occupies their place - simultaneous with pilot position.