Im not sure i understand, are you able to record a video or show screenshots showing the problem? I don't think ill be able to do much about it unfortunately but can always take a look.
PART2: L3 and R3 are bound to the Left Stick and Right Stick Rebind Inputs buttons, (bottom right of that section) you can rebind them so they aren't triggered to some obscure keyboard button like F12, this rebinds the press in, however the sticks themselves cannot be rebound if that is what you mean? I figured there wouldn't be a need to.
PART3: When you rebind these buttons, do they have the same name as each other? When you rebind them do you unbind other inputs to other keys so they are no longer triggered, its not something like that causing the multiple inputs detected?