This is true, but in terms of how the user interacts with the dialog, they can more or less associate the dimmed background and Secure Desktop dialog box with a "from the OS" behaviour. This happens because as you said, the secure desktop is "inaccessible from any other software on [your] computer."
I don't actually know if I fully believe that. I haven't seen the internals of how it's implemented, but at the very least most users can assume that only the OS can bring up the prompt, and only the user can make it go away.