This is a bit ugly, but then I am still way new to programming. This was written in AutoHotKey.
Basically when launched it will ask for the name of the window you want to be able to hide.
It will then watch for your mouse to go over the window you typed in. Press shift while in that window and it will hide.
I chose to do it that way so you could control the window if need be without it disappearing right away.
The window will stay hidden until you either move your mouse to the upper left corner of your screen or
press both the left and right mouse buttons together.
If nothing else maybe it will provide a starting point for someone who knows what they are doing
Both the ahk script and the compiled (exe) are included.