> if we didn't settle on executing compiled machine code exactly as-is, and had a instruction-updating pass (less involved than a full VM byte code compilation)

Apple tried something like this: they collected the LLVM bitcode of apps so that they could recompile and even port to a different architecture. To my knowledge, this was done exactly once (watchOS armv7->AArch64) and deprecated afterwards. Retargeting at this level is inherently difficult (different ABIs, target-specific instructions, intrinsics, etc.). For the same target with a larger feature set, the problems are smaller, but so are the gains -- better SIMD usage would only come from the auto-vectorizer and a better instruction selector that uses different instructions. The expectable gains, however, are low for typical applications and for math-heavy programs, using optimized libraries or simply recompiling is easier.

WebAssembly is a higher-level, more portable bytecode, but performance levels are quite a bit behind natively compiled code.