Perhaps, the proper behavior is the following.

After calling all functions/methods installed at the Python level with 
atexit.register and all C functions installed with Py_AtExit, the 
objects sys.stdin, sys.stdout and sys.stderr are destroyed.

However, the C level files stdin, stdout and stderr are *never* closed 
by Python.  Those will be closed (like any other open file) after all 
functions installed with atexit or defined as destructors have been 
called.