It seems you’re right!
libtool: link: gfortran13 -shared -fPIC -Wl,--whole-archive lib/.libs/libf77_mpi.a lib/.libs/libf90_mpi.a lib/.libs/libf08_mpi.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/wrkdirs/usr/ports/net/mpich/work/mpich-4.3.1/lib/.libs -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 lib/.libs/libmpi.so -L/usr/local/lib -lhwloc -lfabric -lrdmacm -libverbs -lexecinfo -lpthread -lepoll-shim -ljson-c -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0/../../../../../x86_64-portbld-freebsd14.2/lib -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0/../../.. -lgfortran -lquadmath -lm -lc -lgcc -lgcc_s -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libmpifort.so.12 -o lib/.libs/libmpifort.so.12.5.1
In the gfortran case it properly appends -Wl, to these flags. So I guess it is libtool that should be fixed to properly handle Flang as a compiler.
But the point about -fstack-protector-strong still stays.