PHP is native in the same way Python, Red, Java, etc are native. They have a VM, but otherwise interface directly with the OS.
It is in no way similar to JS/HTML in a browser (or Electron).
Is Nodejs native?
JS executed in a browser is not. The constraints were pretty specific.
PHP itself is more native than that in the sense that you can basically run PHP scripts on top of your OS, just like Python or Ruby
How is that not true for JS given node?
It's technically true, but JS/HTML is different from Node. JS/HTML is interfacing through the browser's DOM, while Node interfaces with the operating system itself.
But you specified JS/HTML, that's through the browser, and it doesn't have APIs for interacting with the OS as a normal language runtime does. JS on Node is about the same as PHP in this regard.
You can have script interpreted by a binary. Without a browser involved.