With some hand intervention, it is possible to build 32-bit ATLAS libraries under cygwin64 using the 32-bit MinGW compilers, however. To do this, do your configure as normal, but before starting the build, hand-edit the created Make.inc. Look for the make definition for XCCFLAGS, and you should see that it includes a -m32. Change this to -m64. You should now be able to invoke make as normal.