WODI now officially supports cygwin64
The 64-bit version of cygwin is quite new and not all packages have been ported to it yet. However, all packages that are required to run WODI have already been ported.
WODI packages are usually native windows applications. They are independent of cygwin and you can use them with any version of cygwin. But there are a few build related tools and bootstrap programs, that are linked against cygwin1.dll; they required cygwin in a particular version. These packages have now been updated. They are shipped in two versions (32-bit and 64-bit) and the right binaries are chosen during the installation process. You can use the 32-bit builds of WODI with 64-bit cygwin, or the 64-bit builds of WODI with 32-bit cygwin - or any other combination.
The graphical installer will continue to install a 32-bit version of cygwin for some time, because this version is more stable and more packages are supported. But if you install WODI from console, the install script will now detect cygwin64 and configure WODI accordingly.
If you are already using cygwin64 with WODI, just add the following line to /opt/wodi(32|64)/etc/godi.conf
CYGWIN_WORDSIZE = 64
and upgrade godi-tools to the latest version.