For a configuration language, comments are absolutely crucial. You want to be able to say "# This option is set because <so-and-so>" to explain why you are configuring it this way to the next person that reads the code (or you, in the future).
If the price to pay is that there is some risk some dummy might start parsing the comments as code, so be it. This is not a really a problem in "regular" programming languages, I don't see why it would be in a configuration language.
I don’t think the Linux one is that stupid, but it might be me.
It’s not a “magic comment” because it doesn’t depend on the runtime. It specifies an interpreter to use, regardless of the language of the file.
Eg you can use #!/usr/bin/python for a Python script. I don’t find it worse than the existing alternative of making the file name magic and finding and interpreter based on that.
It's a comment ignored by the interpreter (bash, python, whatever).
The kernel just says "Hey! You can't execute a text file, you weirdo! I'll just read the very first line of the text file and if it happens to be a comment that points to another executable, I'll run that and pass it this file."
