That's cosmetic, the transformation only transforms the object's origin. To complete the illusion of the circle being a sphere the circle's origin would need to be moved to the bottom.
In your capx you can fix it being off center by not moving the canvas' and have their origins be in the center.
canvas1: set angle to 0
canvas1: paste layer
canvas1: set angle to 45
canvas2: set height to 480
canvas2: paste canvas1
canvas2: set height to 240
You'll probably want to make canvas2's height to be twice the screen height so stuff will be drawn from the top to the bottom.
Still in order to not have empty triangles in the corners you'll have to make canvas1 much larger than the screen (that could probably be calculated but it's probably easier to guesstimate).