Currently the problem persists on missions and on instant action, multiplayer for instance works fine. As for the 2-stage issue, mapping a button for that is the same as for weapons release, does not work under the 2 modes. And i just rechecked the nosewheel steering, only works on multiplayer and tutorials, same for every other button bind to joystick.
So as long as either flying tutorial or MP everything is fine, under any other game mode none of the keybinds to joystick works.