The LLVM ports do not include various standard C/C99 headers because of this patch: <https://cgit.freebsd.org/ports/tree/devel/llvm17/files/patch-clang_lib_Headers_CMakeLists.txt>

My specific problem is that this prevents Wine from using LLVM/clang from ports as a PE cross-compiler. In this case Wine uses clang in the 'x86_64-windows' mode, configure does a check in this mode and tries to build a sample file which includes <stddef.h>, and this fails.
LLVM/clang packages on other OSes (Gentoo Linux, macOS Homebrew) do include these files.

And more generally, anyone trying to use ports LLVM/clang to target a  freestanding/bare-metal environment would not be able to use any of these standard header files.
E.g. for a very simple test.c:
#include <stdint.h>

uint64_t hi(void)
{
        return 1;
}

and build with:
$ /usr/local/bin/clang --target=arm-none-eabi -nostdlib -o test.o test.c