I've done a bit more digging. It seems that microcode compilers are known as microassemblers (or meta-assemblers). Issue being that the ones that support modern x86 CPUs appear to be proprietary and not available to the general public. More information here:
Here's a list of Intel CPUs that support microcode updates:
Also, from that same wiki page, it appears it's possible to update microcode at runtime, on Linux at least.
If we had an open-source microassembler we may be in business here. Even if it only supported a single x86 CPU it would still be useful, as you could (potentially) use that CPU to create a new 68k accelerator for classic Amigas (or any other device that used a 68k CPU). This is the only existing open-source microassembler/meta-assembler project I've found so far, no idea what it supports: