Very good question. First though, water gets up there all the time from underneath as well, so it's not like it's a completely dry and rust-free area, but with the lid in place you are seemingly more likely to get more water slipping by through the hood slots and on to that area.
The good news is that there is drainage still, but the bad news is that this drainage has never been the best, and why rust is an issue in that area in the first place.
The rubber seals around the stock vent are primarily to keep engine compartment fumes from entering the cabin, but certainly do double-duty as a way of reducing water intrusion.
I've never tried it, but I don't see why you could not also use the stock type seals either glued to the lid of the Z-Box, or glued to the underside of the hood. It would make total sense. Assuming of course that the lid is even remotely at the same height as the stock vent. Which I've never measured. Don't know about the others though, so maybe they can chime in.
As a side note, it's a good idea to also try to seal the box against the cowl too, as there is no real gasket or seal, other than a tight fit, to keep standing water from leaking past the interface. Some silicone sealant would work just fine in that case.
So maybe someone can set a stock seal up in place to see how it fits? Be good info.
I had one in my trunk up until Monday, but left it back at WH so don't have it to measure or compare.
Let's hope for a positive answer to your question.
But you may be the one to provide it!
Paul
