Small (10cm x 10cm) 2 layer PCBs only cost about $2 these days ($6 for 4 layers), which makes more complex designs possible for hobbyists. However, I am impressed at the hand soldered build by the author! Prototyping on breadboards is so much more accessible with CPUs that are only clocked at a few / tens of MHz and don't have thousands of pins... Looks like hours of fun!
It's true that 2 layer boards are very cheap, but there's a big jump in price when you go to 4 layers, and 5+ layers and beyond is a huge jump in price. I think that for PCI, below 6 layers will be tight and below 4 layers would be impossible.