But the thing was, you can assign the buttons to other keys right?
Absolutely! I have my two trackball buttons wired to player 1's 5 & 6. In Mame's ctrlr default def, I define button 5 as input Mouse_button_1 and 6 as _button2. In Windows they perform just like the left- and right-click. In Mame, they are seen as buttons 5 & 6.
I have my Pause button (upper left button on yours) wired into the I-Pac as button 7 (as I only have 6 buttons on the CP). The I-Pac sees that as a 'P' as well as the Shift key, to make all your admin functions work. Then just assign the Shift functions you want to the buttons that are the most convenient. It's a lot easier than I make it sound. Very nice configuration utility handles it all.
By redefining keys in software, you eliminate a lot of button clutter. That's just what I did. It's ultimately your controller so make it however you wish. As you can see in all the examples on this site, there are a lot of differing designs, all which work just fine.