I think the idea is that the convention of different executable formats each with their own loader should be abandoned in favour of something closer to the machine representation. Frankly I haven't done anything that low level to be able to say how much merit this has, but on a surface level it sounds reasonable.
I was under the impression that APE encapsulates the full binaries for different OSes completely. I don't understand enough about it to be able to tell either way though.
