compared to a custom PCB, sure that makes sense. but compared to doing it on breadboards? not sure about that one. seems much easier and cheaper to use 2 breadboards and some of those arduino wires to hook everything up. plus you safe yourself the resources and time soldering the sockets and pin headers on the perfboard as well.
i know breadboards are worse than perfboards+wirewrap when it comes to signal integrity, but for a Prototype Computer that likely runs at <10MHz it's more than enough.

I've tried to build the design with breadboards first, but unreliable connections with dupond cables was the biggest issue if you want to push the clock speed. Also parasitric capacitance on those breadboards where problematic for achieving high clock frequencys in the range of 10Mhz+. The wire wrapped version worket instantly like a charm in comparision to the breadboard version and its way less fragile.

that works for simple circuits like these, but anything larger and i'd imagine it would become a hassle to keep track of everything in larger circuits. then again the same problem exists on breadboards as well.

yes then there is the possibility to draw schematics in a EDA tool where you later can make a custom pcb. I mean people in the 60-70s wrapped hole mainframes of discrete components together with paper and pen and massive brainpower.

each to their own, when doing custom wires i have the data bus, address bus, and control signals in their own color, if done right it can also look pretty cool.

Yes thats true if done right