Hi I ran into exactly the same issue. Luckily a post on the launchpad site for the arm-none-eabi-gcc toolchain put me onto the answer.
You need to pass into configure the linker options you would normally use in your makefile, eg.

./configure --host=arm-none-eabi CFLAGS="-O3 -mthumb -mcpu=cortex-m4 -lc -lrdimon -specs=rdimon.specs"

and of course change the above to whichever Arm MCU core you are compiling for.

Depending on what you are doing you might also want: --enable-static --enable-debug

However now that I have the configure script working, the actual build fails not finding standard headers:

  CC       src/src_libcyassl_la-internal.lo
  CC       src/src_libcyassl_la-io.lo
src/io.c:84:36: fatal error: sys/socket.h: No such file or directory
compilation terminated.

So if anyone has a clue about that I'd be happy to hear.