Consider the setup where the crank is used for steering and B is the primary action, usually throttle. Star sled, hyper meteor and my own game Gravity Express all feature a triangular spaceship that employ this scheme. Omaze also uses the B button as primary + crank rotation.
While you are playing, the left thumb is resting on the B button. Let's say you get a game-over or level-complete screen. What button should then confirm to retry / go to next level? It might seem most natural to use B, so you can keep holding the PD the way you are.
But Starsled and Hyper meteor chose to match the System software while in menus: A confirms, B cancels.