I'm not affiliated with Gimp and don't know why they didn't support fat binaries in the end; but I did look into compiling Gimp as a Universal Binary on my own at one point. My experience matches those of another comment, which is that not all dependencies supported compiling to fat binaries (i.e. you couldn't just add a bunch of flags and get a fat binary at the end). The only solution I thought of was to compile for both platforms and then lipo all the built files. The main problem is I couldn't figure out a strategy to do this without making the build scripts into a gigantic mess.
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