Ok. I did not read the diagram properly. I thought those were the blanks, not the 2x additional white spaces with the other buttons.

If there are already holes in the cabinet for 6x buttons per player, I would fill them up. No reason to have holes on the top of your control panel. That would be awkward.

You do need 1p coin, 1p start, 2p coin, 2p start buttons so it makes sense to use the ones on top for that. Some games won't have separate buttons for 2P coin, but the ones that do, need the button to work properly.

With MAME and other emulators, you assign any function of your choosing to the buttons. Some game will have random additional buttons that are not used for other games, so it's good to have options. If you look at the button configuration for specific games it will show you which buttons/controls are assignable for that game. I would suggest looking into your favorite games and playing around with those settings while you wait for your orders to arrive.

You can also wire up an arcade button to the power of the computer for turning it on if you want. Something like this would plug into the motherboard and give you leads to solder the button wires to. https://www.amazon.com/NOYITO-Motherboard-Extension-Silver-Gold-Plated/dp/B07BVV3G15