Most or all references to setuid in the article are to the permission bit, not the function call. The parentheses are a bit unfortunate.
That said, the setuid bit and the setuid() function are quite intimately connected: setuid() allows a program to drop privileges that might be elevated by means of a setuid bit. Either one does not make much sense without the other.
The main reasons why one should consider not using the setuid/setuid() mechanism are that it is not widely understood and not very portable. See, for instance, this paper (PDF).
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