I'm developing arcpy scripts in PyCharm, though I have also tested this in Wing IDE and it does the same thing. Is it normal that when you use arcpy.AddMessage() it prints to your console output? I know it does not do this in PythonWin (or it used to not do that ~2 years ago when I was using that IDE). I thought that AddMessage only allowed messages to show up when running the script tool in ArcMap, not in the console output and that's why you use AddMessage and print statements together in stand-alone scripts, so that way if you run it in a python IDE, you still get the messages.
Note: I do not use arcpy.GetMessages() or GetMessage() anywhere within the script.
I am running 10.5 (python 2.7)
will print this in the output window: