I think you misunderstand 3d printing costs and time. $20 gets you an entire kilo of standard plastic for printing. I highly doubt his enclosure setup took more than 50 grams to print, or about $1 total. Total printing time was likely under 5 hours.
PCBs are over an order of magnitude more expensive and generally have a two week lead time unless you fab them yourself on a cnc or laser setup. Also, what do you do if you realize you messed up something in your PCB setup? You have to wait for a whole new batch or else toss it and wire manually anyway. With 3D printing, you just modify the model and print a new version in a couple hours.
For one-off prototypes like this a custom PCB is a really iffy proposition.
