For a start it is not because TCP/IP has taken over the world that it is perfect. There were also strong (and valuable) non-technical reasons for this success. But even then...
Since UDP is available (and pratically the same as "raw IP"), TCP is not forced on anyone. TCP is much more like a library than a midlayer, in theory AND in practice.
As for IP, it was designed to be the lowest common denominator of every networking technology, so it could run on anything. That is why it is called _Inter_net. It is the lightest and less constraining networking midlayer you can think of (and also the most featureless one).
So I think the example of TCP/IP fits the thesis of this article quite nicely.
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