I'm guessing the Spartan II was used because it is compatible with 5V IO

Spartan 2 was used because it was free, author salvaged it together with Atmega128 from some scrap he had laying around :)

Here is a prototype https://imgur.com/gallery/486-homebrew-computer-lsUiWdw

The most impressive part of this build is that maniek86 (Piotr Grzesik) is still in High School (electronics oriented CTE).