Now that the power supply would be above the top shelf and out the way, I could decide where I wanted to mount the motherboard tray. Because the tray I chose was ATX, it was quite tall. So tall in fact that if I mounted it as high as it will go, it only just avoided the start of the curvature of the bottom edge of the case.
After some Photoshop work, the area that needed to be removed from the back of the case was cut and the tray slid in a treat. The corner of the tray was also cut so that the leave to open the case could be accessed. The fit was so good, the top edge of the tray was flush with the top shelf.