The configure test essentially looks like this -- could you try this manually and see what happens?

cat > conftest_weak.h <<EOF
int real(int i);
int fake(int i);
EOF

cat > conftest_weak.c <<EOF
#include "conftest_weak.h"
#pragma weak fake = real
int real(int i) { return i; }
EOF

cat > conftest.c <<EOF
#include "conftest_weak.h"
int main() { return fake(3); }
EOF

# Try the compile
clang $CFLAGS  -c conftest_weak.c
clang $CFLAGS  conftest.c conftest_weak.o -o conftest $LDFLAGS $LIBS

The configure test rules that weak symbol support is there if both compiler invocations return an exit status of 0.