The additional ports are for expanded functions beyond the basic functionality and Inventables has teased some of the add-ons they plan to offer on their blog: http://blog.inventables.com/2015/05/a-sneak-peak-at-x-controller.html
As such, I’m guessing the other holes are for future use when these options become available.
the buttons on the front do function with the stock x-controller during normal operation, here’s a thread where someone made their own for the original controller: https://discuss.inventables.com/t/feed-hold-resume-hard-buttons-only-sometimes-working-resolved/22659
that will hopefully help with understanding what they’re for.
Me personally, I put together the side board, then put it back in the box. not because it’s bad, but because I already had made a custom stand with the controller mounted in a rack drawer below and couldn’t get the cnc with sideboard to fit on the top without blocking access to my keyboard on the side. I will eventually use the rails for it to give some extra support to the waste board.