Except isn't X86_64 ISA technically property of AMD, not Intel?
I know some of the later stuff (SIMD / AVX / SSE / etc) is Intel, but technically I think they could leave that off and still be successful assuming that would be all that's needed to not be infringing (which I don't know if that's the case or not).
Software emulation is fine (otherwise QEMU would be pretty dead), it's just hardware accelerated emulation and actual HW implementations of the ISA that Intel does not like.