First of all nothing in the article is about optimization. Scala does not even have an optimizer…
It was about translation strategies and macro expansion.
But this makes no difference. You have all issues you just named exactly the same in so called "high level languages" as you have in C. C is in fact a high level language, and the code you write in C has not much in common with what the machine actually executes. The last time this wasn't like that is about 40 years ago.
1. Whether the C optimizer kicks in or not is pure dark magic. Nobody can tell from just looking at the code. The optimization techniques are way too complex to be understood ad hoc, not even experts can do that.
2. The difference between the optimizer doing its work, or instead the computer just verbatim executing whatever someone written down is hilariously large! Adding -O2 can make your code many orders of magnitude faster. Or it does almost nothing… (But like said, you can't know what will happen just from looking at the code, that's point again 1.)
3. You neither can express what the machine does in C. The machine does not execute anything like C. The last time it did is over 50 years ago… Since at least 30 years we have kind of JIT compiler in the CPUs which translate the result of compilation to ASM into the actual machine language. A modern CPU needs actually to emulate a computer that still works like a PDP-11 to match the C machine model even the real hardware does not look anything like a PDP-11 any more! You have only very indirect influence on the actual machine code when writing C. It's mostly about forcing the CPU internal JIT to do something, but you have no control over it, exactly as you don't have control over what for example the JVM JIT does. It's the exact same situation, just a level lower.