The marks on the caps is that someone checked the polarity of them before they power it up. It usually means that the big components there were placed manually on the assembly line, and to avoid popcorn capacitor, a second person checks the polarity.
Otherwise... Yes, nice design, and overkill. Which is probably fine. That 500 buck FPGA probably sold fraction of that price anyways, so why bother redesigning it. Power supply designed in house...I would really like to design boards, where I got enough space, enough money and a big team.