That's because a HDL is not a lower level machine language, but instead they are languages used to implement a machine that consumes a machine language.
Consider what happens when you implement a x86 emulator in python: you're using a high level language to implement a machine using a particular substrate (a simulation inside another machine). This simulated x86 CPU executed machine code and you'd call that machine code to be the "native" or "lowest level" language with respect to that particular machine.
You can see how that choice of machine language bears no relationship with the language used to implement the underlying machine.
Consider what happens when you implement a x86 emulator in python: you're using a high level language to implement a machine using a particular substrate (a simulation inside another machine). This simulated x86 CPU executed machine code and you'd call that machine code to be the "native" or "lowest level" language with respect to that particular machine.
You can see how that choice of machine language bears no relationship with the language used to implement the underlying machine.