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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.exe that includes high quality but "non gpl compatible" AAC encoders. Or to build a custom FFmpeg (just modify its configure settings in the script). 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 then legally redistribute the binary you create. But alas 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.
Ping me if you have any feature requests.
You can also install it faster by downloading a (32 bit Ubuntu zipped version) from https://sourceforge.net/projects/ffmpegwindowsbi/files and unzip it to /tmp. Voila, the compilers are already built, now do a git update, then run the ./cross_compiler script.
Another way to get faster installation is that I've got it set to build the cross compilers with only one cpu currently, so you could go into the script, search for where it says "--cpu-count=" and adjust that to get it to build more quickly.