Among other things, JavaScript in the browser has no way to even express "kill PID 1234 on the user's machine" or "list the contents of `C:\Users\Documents` and upload all of the files" or "spawn cmd.exe on the user's machine". How would you even do these things if you could run any JavaScript in the browser? You can't.

However, chrome.exe itself does because it's a native application, as is the sandboxed JavaScript interpreter inside of chrome.exe.

(This is a very oversimplified explanation but I think this is the disconnect people are having)