Likewise no problems compiling using an older version of clang (Xcode 
5.0.2), but I do see that flag

bizarro% clang --version

Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

Target: x86_64-apple-darwin13.3.0

Thread model: posix

It looks like it's in there.  There is a test to check (see below) but the 
compiler doesn't fail, it just warns so the test is perhaps concluding that 
yep, supported which is technically true.

bizarro% find . -type f -exec grep malign-double {} /dev/null \;

...

./deps/fftw-3.3.3-double/config.log:clang: warning: argument unused during 
compilation: '-malign-double'

./deps/fftw-3.3.3-double/config.log:configure:14242: clang -stdlib=libc++ 
-mmacosx-version-min=10.7 -m64 -c -O3 -fomit-frame-pointer -mtune=native 
-malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math 


...


./deps/fftw-3.3.3-single/configure:$as_echo_n "checking whether C compiler 
accepts -malign-double... " >&6; }

./deps/fftw-3.3.3-single/configure:      CFLAGS="-malign-double"

./deps/fftw-3.3.3-single/configure: CFLAGS="$CFLAGS -malign-double"

./deps/fftw-3.3.3-single/configure:     # -malign-double for x86 systems

./deps/fftw-3.3.3-single/configure:      { $as_echo 
"$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts 
-malign-double" >&5

./deps/fftw-3.3.3-single/configure:$as_echo_n "checking whether C compiler 
accepts -malign-double... " >&6; }

./deps/fftw-3.3.3-single/configure:      CFLAGS="-malign-double"

./deps/fftw-3.3.3-single/configure: CFLAGS="$CFLAGS -malign-double"

./deps/fftw-3.3.3-single/configure: { $as_echo 
"$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts 
-malign-double" >&5

./deps/fftw-3.3.3-single/configure:$as_echo_n "checking whether C compiler 
accepts -malign-double... " >&6; }

./deps/fftw-3.3.3-single/configure:      CFLAGS="-malign-double"

./deps/fftw-3.3.3-single/configure: CFLAGS="$CFLAGS -malign-double"

...

Binary file ./usr/lib/libfftw3.3.dylib matches

Binary file ./usr/lib/libfftw3.a matches

Binary file ./usr/lib/libfftw3f.3.dylib matches

Binary file ./usr/lib/libfftw3f.a matches

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