Yeah, the entire system is re-emulated using 68k uae on a "68k" system.
Unfortunately the jit cpu emulation in uae assumes little endian byte ordering, but you couldnt use the jit code path for amithlon native uae. That said though even interpeted emulation would be faster on native x86 amitholon vs completely emulated with amithlons 68k emulator.
As yet there's not a great deal of amithlon natively compiled software, so Id be a happy man if Vice does end up getting an amithlon version.