This might be a dumb question but what would happen if you used touch up paint on an area that already had surface rust and did not remove the rust. I assume it would get worse and you would know it pretty quickly.

You would get a horrible finish, the paint would flake off, and the rust wouldnt be fixed. Bondo of rust does not fix rust, nor does paint. Rust is like cancer, and it will continue spreading until you remove it.

Prep the area correctly, then use touch up.