Did you change anything at all in the demo? That's so strange, I don't have that happening on my end. It looks just like a z-order issue with the phone case being too low. Does changing the window's aspect resolution impact it at all (ex. shrinking the window make it go away)?
The only thing I changed is renaming the inner folder to Game so Renpy can run it, and putting the game in the same folder as my other renpy project. though I re-downloaded and it's still the same thing. But I think I figured it out. in the message_viewport, you defined the ysize to be 750, so I removed that line and it somehow auto-scaled on its own with the correct ratio O_O