Here's a how-to for reproducing this bug on Sierra:

1. Install Xcode 7.3.1 (All 7.x should be fine)
2. ./configure --enable-universalsdk=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
3. make

On Benjamin's question:

> why does configure define HAVE_SYS_RANDOM_H if including sys/random.h causes an error?

autoconf defines several "default includes". For example in line 592 of configure:

#ifdef HAVE_SYS_TYPES_H
# include <sys/types.h>
#endif

And in line 5559:

# On IRIX 5.3, sys/types and inttypes.h are conflicting.
for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
		  inttypes.h stdint.h unistd.h
do :
  as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
"
if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
  cat >>confdefs.h <<_ACEOF
#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
_ACEOF

fi

done

The check for sys/random.h starts from line 7758, so sys/types.h is already (accidentally) included when checking it.

So, here's the fix.