It is more of because when your keyboard shortcut is set to that, the command given to the computer is only to shutdown the default way, which Apple made it to reopen windows when logging back in. And when u said that it was a preference to reopening windows when logging back in, it is not a preference. It is more of a question whether u want to reopen when u are shutting down/restarting your computer.
I also have a similar problem, but it is not about the keyboard shortcuts. I want to create a program to help restart into bootcamp, but when I restart back into Mac OS, it helps reopen the windows.