It’s easier to do pcb-layout wise. Allows you to re-use most components between board revisions, or when you’re done with the project. Probably less ewaste overall because of that.
Not only would designing a fully custom board require a lot of error-prone effort, getting a lot of components in tiny quantities can be prohibitively expensive.
Good engineering includes optimizing for cost (monetary and non-monetary), and I'd argue that for many hobbyist one-off projects that won't be manufactured at scale, dev-boards-on-PCB is good engineering.
This is also a hobby project. To custom build a PCB with all of the components brings this into the Kickstarter world of something. So the person can buy <5 PCBs to play with as hobby or attempt to fund say minimum 500-1000 pieces. From TFA: "Important Notice: This is just a fun project, it was started to pass the time, it is not at all professional and is not intended to be. Is not an alternative for professional device."
Even with the method chosen, if you think the person did not become better after making the simple PCB or any of the other coding required, you're off your rocker. Every build like this comes with mistakes and learning how to correct them.
- Certain things need good layouts - I think I can see a DC-DC Converter, you need to minimize certain loop areas, etc. You also need to ensure that you use the correct footprints for the chips. Way easier to just use a bunch of modules with a simple pcb.
- It reduces the components you need to aquire - you need to select a inductor with the correct specs for the dc-dc converter, a bunch of different resistors and capacitors for all sorts of uses or you just purchase a cheap module from china.
- It's easier to solder. Fancy chips with packages with no leads are not trivial to solder. LED's might be a bit sensitive to temperature and can get destroyed by a not-so-great solderer. Small pitches on IC make it easy to create solder bridges or bad connections.