I'm not sure you understood the point. It means nothing to claim that deep down it's all opcodes or electrons flowing. What matters is being able to transform the code targeting the high level interface to the lowest level interface in a way that remains usable and regression-free. Sometimes compilers for widely popular languages introduce bugs and weird behavior too.
Compilers introduce bugs, yes. Compilers are code, and code can have bugs and regressions.
But the comments above make no mention of bugs are regressions. They said compiling php into machine code is "impossible."
Going form high level interfaces to lower level is the easy part. It's what all interprets and compilers do already.
Having different intermediate forms is also a very common practice. There is nothing special about php here. Except for maybe it's underserved reputation of being an obtuse language.
If it is running on your CPU, then it is running on your machine.
When the compilation happens can be different (interpretted, JIT, ahead of time) but those are just design choices.