I had a Z3 in a while ago that had the wheel arch splash panels removed for some reason. The mud had sprayed up onto both rear shelves under the rear wings and just sat there. The shelves had rotted and the car was not worth saving because of the rot.
The splash guards are normally fitted near completion and can be forgotten so do remember to fit them. I only mention this because from the photo of the gap around the boot, a lot of damp/water/spray will probably get into the boot as the splash panels won't have been refitted at this point. It may not look as if anything will get in that gap but I can assure you it will.
Looking at the pictures of the red car, the gap doesn't seem so bad, you might get away with some pipe insulation foam (must be the closed cell type), this could be fitted to the top flange to provide a seal depending on how much gap you have.
If you can use the Z3 rear hinges I would, if you don't have any give Spurs in a coupe a shout as I'm sure he will be able to help for not much money.
Nothing shouts kit car more to me than external boot hinges (apart from bolt on fog and reversing lights hanging from the rear bumper!), the problem is that new boot hinges are made of Chinesium and break, old boot hinges are stronger and better quality but most are 50 years old and the chrome won't be great.