Any opening, in particular as large as this is, is a potential leakage point. The cars only done 8000 dry miles so no real evidence on this vehicle.
I'd hate to be caught out in a real down pour with a couple of hundred miles to do.
I like your suggestion of using neoprene as a material that could be easily cut and is self supporting.
For the little effort involved in providing a fix I'll give it a try.