I've long had my suspicions about what's actually happening with this, here's what I think...
I suspect there are actually 2 location and 2 size properties, similar to how text objects have LocalText and Text properties. The commonly used "Location" and "Size" properties are the equivalent of LocalText, i.e. temporary values that are never saved. Scripting size and position changes to these likewise will never be saved.
However, there are other location and size properties we haven't discovered, or just don't fully understand, that are saved if the window is set to UserMovable and UserResizable. The only reason we're getting saved loc and size when changed by a user is that the hard coded event handler is updating both the temp and save values. I'm betting scripted changes would likewise be saved if the mystery save values were updated.
So the big question is, what are these mystery props?
I suspect they are PackLocProp and PackSizeProp, I just have never had the chance to dork with scripting them. Frankly I'm not sure the scripting lang can handle what may be needed to set these properly ingame. I believe some of the atributes for these props are derived form other factors like current screen size to default size ratio. Still, it may be possible to do some basic stuff with it, like pass it to a variable to be used in restoring window state.
Maybe someone with more time than I can play with it more
