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We try to have IDLE work the same as Python (and CPython, where relevant), except where differences are intentional or unavoidable. I am trying to eliminate some unintentional avoidable differences in other issues. However, this one is unavoidable given IDLE's basic design. Also, Steven is correct; see
https://docs.python.org/3/library/builtins.html#module-builtins
IDLE executes user code with "exec(code, self.locals)" (run.py, l.351 in 3.5).
https://docs.python.org/3/library/functions.html#exec
says "If the globals dictionary does not contain a value for the key __builtins__, a reference to the dictionary of the built-in module builtins is inserted under that key."
(Doc issus: From the builtins doc and the Jython example, this seems implementation dependent. Steven, does
 >>> d = {}; exec('', d); d.keys()
 dict_keys(['__builtins__'])
have this result in Jython?)
In the IDLE shell, each statement is exec'ed separately. With two statements, __builtins__ is added back before 'min' , while with one statement, it is not. 
Editor: Run Module execs the entire file at once. I expected print(min) to fail either way, but it works either way. I verified that globals().keys() lost '__builtins__', so I don't know how __builtins__.min is found.
I left this open to consider adding a line to
https://docs.python.org/3/library/idle.html#idle-console-differences