it is part of the move from arcade cabinets to home game machines. Cabinets had the normal controls up top for the game but there were other buttons and switches for controlling the cabinet itself including access to higher level game functions like difficulty settings that weren’t meant to be exposed to the user.

When Atari made their console the user held the controller for the game but there were also several switches on the console itself providing these same higher level functions (reset and game select). Many games required you to use these higher access level switches on the console to do things like select levels or game modes because these games were getting ported from arcade cabinets or just designed by people used to developing for arcade cabinets.

nintendo moved these switches from the console to the controller, and then as game development evolved these buttons became part of the normal controller and software scheme.