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Welcome to the ffmpeg-windows-build-helpers wiki!
Basically this script exists to make it easy to compile your own ffmpeg that includes high quality but "non gpl compatible" AAC encoders. There are many AAC encoders that FFmpeg has, but many have drawbacks, see http://en.wikipedia.org/wiki/FAAC "alternatives"
Theoretically if you compile a local copy of FFmpeg, then you aren't subject to as many licensing restrictions (ex: gpl) as you otherwise would be, so you can (license-wise) mix in more encoders and use them locally, just not legally redistribute the binary you create. But IANAL.
NB that you can get smaller final binaries by removing some of the "--enable-XXX" from the build_ffmpeg method ffmpeg's configure options. Many of them you don't need, probably.
Also note that you can compile 64 bit windows ffmpeg.exe even from a 32 bit Linux VM, thanks to the magic of cross compilers.
Ping me if you have any feature requests.