Reason Japanese carpenters do or did that is that sea air + high humidity would absolutely rot anything with nail and screw.
No furniture is really designed from a single tree, though. They aren't massive enough.
I agree with overall sentiment. But the analogy is higly flawed. You can't compare physical things with software. Physical things are way more constrained while software is super abstract.
The other reason was that iron was very expensive in Japan as they had only low quality iron ore.
I very much enjoy the Japanese carpentry styles that exist though, off topic but very cool.
Some amount of boilerplate probably needs to exist, but in general it would be better off minimized. For a decade or so there's sadly been a trend of deliberately increasing it.
It's rather saying that we should have parts that join without nailing by now, especially for things we do again and again and again and again.