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FEX-Emu 2308 Continues Striving To Be "The Greatest x86/x86-64 Emulator On Linux"
(www.phoronix.com)
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The main difference is that Box86 does not support 64-bit binaries. There is Box64, but it can't run 32-bit. FEX does not have that limitation, which is handy if you want to run Windows games (which are mostly 32-bit) on Apple Silicon (64-bit).
There's also a performance difference. A benchmark from last year showed box86 outperforming FEX considerably in CPU-only workloads (50% faster), but the difference in OpenGL performance wasn't much. There have been several improvements to FEX since, then so I'd expect it would've closed the gap by now.