Copper sheeting had been used on the bottom of wooden boats for years in place of bottom paint. It was always the outside layer with some sort of bedding material under it. So what your proposing has been done, your just taking a little twist. I agree with Bill that you should bed it in something. I have not used it but from what I have read I would not use 5200. I understand it is darn near impossible to remove if you have to take it apart for some reason. I would use Boat Life Caulking or some other polysulfide caulking.

My concern with putting it under the glass is what it something goes wrong? Then your facing a major job to repair it. I don't know what would go wrong though.