I am pretty certain that memset is not conceptually being handled especially different: it is simply being inlined. If you have a memset of a variable to 0, gcc's compiled output might involve just a single mov instruction and if it is a small array, it might be a few mov instructions: if it is a lot of memory being cleared, it might involve a call.
However, as it is inlined, the semantics are pretty clear for how it should work (and attributes like pure will be deduced, as they would for any function you include in your actual code; you don't need to mark it as such <- edit: to be clear, though, that I really don't think that memset is "pure"... it is pretty much the exact opposite of "pure"): it is equivalent to assigning a variable a value, and if that variable's value will not ever be used, then the assignment will not happen.
Instead, if the developer really really really insists that that assignment happen even if, from the perspective of the C language standard there is no legitimate side effect of that operation, the correct thing to do is to temporarily qualify the pointer with volatile and then do whatever it is you wanted (such as wiping it).
Sadly, this article does not even in a single place mention "volatile", so I'm not certain that the author understood how this works. Instead, he states that a "solution" is to instead put a zero in the first element and then copy it to subsequent elements... something that could easily be detected by abstract interpretation, and which a sufficiently smart compiler would be correct in also optimizing away.
a.c:14:2: warning: passing argument 1 of ‘memset’ discards ‘volatile’ qualifier from pointer target type [enabled by default]
Curiously enough, making a custom function with volatile pointer argument and `pure' attribute still causes GCC to optimize it away. I guess such combination makes no sense anyway.
extern void * memaaa(volatile void *__s, int __c, size_t __n) __attribute__ ((__pure__));
However, the author's attempts to redefine memset without using volatile rely on gcc limitations: in the first "trivial" case that it does not use abstract interpretation while looking for constant variables (in this case, it should be easy to fold that loop down to "oh, that rvalue is always a constant 0), and in the second that it does not do extensive optimization across compilation units.
As for the other thing you noticed: while I would imagine that the gcc-specific "I am the developer and want you to do something very special and important" __attribute__ would override any notion that it might have regarding "volatile", they are really orthogonal concepts: with just that prototype the compiler wouldn't even know if that function does anything at all with the memory you passed... the function might just do something with the pointer value and not indirect it at all; therefore, one would pretty much demand that "pure" have the semantics that gcc is giving it here.