Well the big problem AROS has is in the byte order (as you are probably aware), so this is the best option 
Not only the byte order but also the size of certain C types and the packing of C structs. This makes the integration layer more involved than on PPC MorphOS and AOS4. Some people advocated to change the native i386 endianess like amithlon did but majority decided to not reduce the native x86 performance for better m68k software integration.
I am still sceptical that emumiga will always be able to guess the translation of C structs between the two worlds (m68k and x86/AMD64/...) without knowing it at emumiga compile time. But I have been proven wrong in the past.
greets,
Staf.
