@Piru
The obvious solution would be to wrap it all inside an amiga 68k executable with a small 68k code stub that determines the actual runtime system and loads the appropriate ELF, except that AROS does not run 68k binaries at all.
No need to use 68k code. MorphOS executables are always executed from the beginning of the first hunk and OS4 executables are executed from _start() entry.
I would probably just use simple script to detect OS. It would do everything what fat binary would do.