It was weird in a Nintendo way, yeah, but imo there was hardly anything illogical about it. The triple handle setup was reasoned in the way that if there was a more “classic” control scheme in the game, you might use the d-pad instead of the joystick (which was shit in the way it wore out though). Most games did use the joystick, but not all, and not all the time.
I think the reasoning was to have more adaptability in traditional Nintendo sort of way.
Also, the Dreamcast controller looks very weird as well, has less buttons and came out two years after.
https://www.britannica.com/topic/Homo-sapiens-sapiens