It seems pretty cut and dry to me.

1. C99 defines that double underscored tokens are reserved identifiers in the implementation of C99.  

2. C99 is defined by both the compiler and the standard C libraries defined in C99.

3. unistd.h is not part of C99.

Unistd.h is therefore clashing with a C99's totally valid usage of a double underscored and reserved name.  Yes, unistd.h is shipping with a libc implementation, but nowhere does it say in C99 that that's an excuse for utilizing the C99 implementation's reserved namespace.

One could question whether it is a good idea or not to tell the users of your C99 implementation to have to use extensions to the language via the use of double underscored names, but it really does say in C99 that these are there for ANY use by the implementation.  This means that if you see double underscore'd identifiers in a user's code, that this code is at worst "not portable to other compiler environments".  

Dave