So I couldn't figure out why the roof box cover plate was such an odd shape...
Roof Box Closing Plate.jpg
Why the holes - there's no bolt holes or anything in the roof. Why the odd shape - the hole in the roof box is a straight forward rectangle.
But then I spotted this...
Engine Latch Cover Plate.jpg
Oh, so its a case of close enough fit!!! I mean why not use the plates from the Engine Cover Latch access in the roof box?
Is this a factory feature or perhaps something that was added later? I would have guessed that it might have been designed with some sort of giant grommet like plate. Of course it might not be stock as somewhere in the history of this car the roof box had been opened and all sort of strange magic applied to fix a leak.