al_get_window_position(...) returns the client rectangle x and y coordinates and not the actual window coordinates.

When you do following to window with borders:

al_get_window_position(display, &x, &y);
al_set_window_position(display, x, y);

You will notice that it moves.
It also happens with frameless windows when you run the program in a sandbox (tried avast! Free Antivirus autosandboxing).

I only tested it on Windows with allegro 5.0.7 so I don't know if the same behavior applies to Linux and Mac.

Is this a bug or intentional?

IMO, if that code causes the window to move, then Allegro is buggy.