The package mingw-w64-x86_64-python2-cx_Freeze correctly creates 64-bit binaries but they are created with an incorrect library manifest which causes them to fail to run on Windows. The library manifest file from cx_Freeze at source/bases/manifest.txt always sets the arcitecture to x86 when it should be amd64 for 64-bit builds. This resulsts in invalid base executables in site-packages/cx_Freeze/bases/. It is very difficult to track this bug down when you don't know why your binaries fail to run on Windows.
Fortunately this is easy to fix. Running sed -i 's/[xX]86/amd64/g' source/bases/manifest.txt in the cx_Freeze source tree before building it is enough. Presumably this could be added as a patch applied before the package is built by makepkg.
This is probably also an issue for upstream.
Works for me at the moment, so probably fixed. New issues can be filed on GitHub.