IDLE doesn't control window placement - that's left to Tk to handle.  
Hopefully it will get better with time.  Once you take control, you 
have to handle all the window placement, which is one of the things 
that window managers are expert at, supposedly.  You could try taking 
your issue to the Tcl/Tk devs.

I'm running 8.5 here on a netbook with XP and a 1024x800 screen.  I 
simply reduced the initial height to 33 using the Configure dialog.

Zooming the window height is also helpful.  Use the hotkey.  Some 
attempt to control position  by platform has been made in 
ZoomHeight.py, where you'll find some magic numbers.  

On Linux, some people have panels at the top, some at the bottom, some 
hide them, and some don't have any.  Maybe we'll look at this config 
again once we get the extension parameters on the Config dialog.  We 
could move some of those magic numbers to the config file.