Compared to commercial, what he's got is:
1. Lighter (2x4s are light)
2. More robust (2x4s are tough)
3. Looks better (An off-the-shelf product would look better in a showroom, but this one fits his room exactly, and fits his equipment exactly; that makes a much bigger difference).
I'll mention: That's true for most of the crude furniture I make. I have fine woodworking, and I have not-so-fine woodworking. The fine woodworking pieces tend to be generic (e.g. a bookcase). The not-so-fine-ones tend to be special-purpose. Right now, I have custom stuff built up for remote work, for example, with cameras/cables/etc. properly routed.
I'm currently planning a studio desk right now, funny enough. I could buy one for maybe €500, but just the heavy duty shelf sliders I need will be €70 for a pair. A pre-bought one will also have a light aluminium frame, whereas mine is going to weigh a ton with steel tubing.
Like you say though, if I make one it will fit the space perfectly etc. All in all it's worth it for me even if I personally don't save money
https://www.homedepot.com/p/Everbilt-18-in-Full-Extension-Si...
They're rated for loads up to 100lbs, and they're plenty tough enough to hold up a full-sized MIDI controller. They're stiff enough too.
If you're worried, though, you can double them up (two on each side). Now, you're at $30. Typically, when you double up, the load-baring capacity more than doubles.
I have a planer, but I didn't use it at all in this project.
Might be regional. US has a ton of land and resources, so maybe wood is cheaper here. You're pricing in Euros, and Europe is a bit more densely populated.
One could build a desk from even better materials than the $1000 desk; maple, walnut, mahogany, stainless steel, brass, whatever. But it wont be <$1000 for materials then, let alone <$100.
I'm in favour of DIY and think it's admirable that you would build your son's desk yourself rather than buy, but I think it's important to be realistic about the costs and materials. These costs were a surprise to me at least, after getting into woodwork/metalwork.