Thanks for the links. The discussion on the first one is interesting, it wasn't clear to me from the original doc that the UNIX version needs to overwrite itself to get to the ELF header. That's a bit unfortunate, because it means you can't share the program again after you ran it the first time on BSD or Linux. Still very clever, though. I imagine there could be a "repackage for distribution" switch added to put the MZ header back again.
I did the research and what we've accomplished here, while imperfect, is the best of all worlds solution. I like to think of it as an installer that takes a few microseconds, because it only needs to change 64 bytes. I've been considering adding a CLI flag where you can say ./foo.com --restore and it'll put the original 64 byte header back in place. Perhaps one day we can change the Linux, BSD, and XNU kernels so they can recognize the APE executable format. But until that happens we've got a great shell script hack that's now required by POSIX which is exceedingly fast and works on pretty much all systems stretching back decades.
If interested, see previous discussions of APE:
https://news.ycombinator.com/item?id=24256883
https://news.ycombinator.com/item?id=25556286