The recent version of cosmopolitan generates ARM binaries for Linux and MacOS (https://github.com/jart/cosmopolitan#arm; mode aarch64). There is also blink that provides the x86-64 emulation layer for (APE and other) binaries on a variety of platforms (https://github.com/jart/blink).
Just created my first ever fat ape executable. I ran `apelink.com -o fat-ape-binary.com o/tiny/examples/hello2.com.dbg o/aarch64-tiny/examples/hello2.com.dbg` to create an executable that runs on Linux+OpenBSD+NetBSD+FreeBSD on x86_64+aarch64.
And x86-64 is a particularly bad bytecode, for one main reason: its strong memory ordering rules, compared to nearly every other architecture. IIRC, simple things like doing a store in x86-64 have an implicit release barrier, while other architectures can freely reorder the stores unless there's an explicit barrier. This means that a x86-64 emulator on for instance ARM has to either be single-threaded (and would still have issues with shared mmap regions), have special hardware support for x86-compatible memory ordering (as found for instance on recent Apple ARM CPUs, and used for their x86-64 emulation, but not common elsewhere), or add explicit barriers everywhere (which kills the performance).
The only real advantage of x86-64 as a bytecode would be that it has less registers than most other architectures (only 16 registers, while other 64-bit architectures usually have around 32 registers), which allows a 1:1 mapping of the registers on the emulator while still leaving plenty of them free for temporary use.