Presumably Joust, Klax, etc had 2 joysticks, with Joystick 1 mapped to Joypad 1, likewise with Joystick 2 mapped to Joypad 2.
Maybe the original Galaga machine only had one joystick, which is mapped to Joypad 1. As there was no Joystick 2 on the original machine, the game expects players to share the same joystick.