It is rather stunning that PCI signalling works despite this style of wiring, but the proof is in the pudding! Dealing with the wire inductance and the interference between the signals could easily be the hardest aspect of this implementation. Probably much harder than designing the logic itself. IIRC, the absolutely minimal working PCI hardware and software could actually be rather rudimentary, if one did not need implement the entire PCI specification in a compliant way.
This is really neat and something I thought about myself.
An OS that would run on this is Inferno, though I am not sure of the state of the 68k compiler.
Look at all those wires! No wonder hobbyists haven't bothered with the PCI bus much.
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.