If you're doing production work then sure, you will need that kind of optimization to stay in business.
But if instead you are looking to produce one-offs with relatively low skill and a limited amount of money to spend on tooling then I totally see the point in making things from re-usable and easy to size components.
And then there is the garbage disposal element: almost none of this is waste, even at the end of life of the original object. The same goes for Lego, all it is is parts, and parts have a life of their own (in the decades!) that is totally different from the life of the objects made from them (minutes to several years).
So the over-design and the over-thinking go towards doing that work once so that the users of the system won't need a tools budget in the 10's of thousands of dollars (welder, plasmacutter, grinder, machine shop to go with it) and still build functional equipment that is not readily available.
As for how sturdy the bed frame looks: that's mostly a function of the design of the frame, not of the parts that went into it (Ikea sells kids bedframes that look quite close to what is shown in the article), you could do a much better job if you wanted to with the same parts.
I also note a lot of 'cheating' where the system doesn't work anymore (for instance: the stays to stabilize the bed and the legs under the sled).
And the strength concern is all the holes weakening the very spindly looking frames. I'm not bored enough to do the stress calcs, but it doesn't look sturdy enough that I'd trust a kid on that bed.
170 AMP harbor freight welder -- $125 160 AMP Arc welder, amazon $199 CUT-50 Plasma $225 Pizza style air compressor, on sale HF $49 this weekend Angle grinders - I have a bunch $39-59
Anyway I need these tools because I am constantly breaking my farm equipment. Also, instead of diddling around with things I just tack weld things, like my plow blade broke off I couldn't find the bolt so I just welded it in a few spots.
The CUT-50 and the cheap AC/DC arc welder are the best tools, but I use the MIG welder as my first go-to
I "modified" the arc welder to make small metal molds in a carbon crucible. I use aluminum, but it will melt steel. I can lathe/mill that to what I need. I also have the cheapest HF mini lathe and a nicer mill. So yeah all this stuff cost me $2000-$3000 but I use it. I also have a completely different CNC setup.
They made a kit called the Elektor set in the 1940s-50s, my dad gave me, it is the same concept as this post.
I can certainly understand that mental blindspot however given I can't help but think of enterprise software as drastically overpriced for stuff I could slap together myself.
I would use open modular hardware if it were available everywhere like plain metal stock is, but it's not so I've learned to improvise.