I am just now fabricating this sort of outside transom cover from 1/8" 5052 AL. I will be using most all of a sheet that is 18" x 60". It will be cut and shaped on top to fit just below the transom cap and will extend to about 2" below the rivet line for the Z brace, which I have removed to clean up. In width it extends to just beyond the transom eyes on either side. If you do it this way, and with 5200, as you plan, the replaced Z brace rivets should seal the bottom pretty well and not interfere with the transom wood inside since they are below it. Additional clamping will be done by the knee brace and other through bolted hardware, and the splash well drains will also hold it. I plan to do as I have seen others do and after the transom is in, stainless steel screws around the perimeter of the plate and into the transom material but not through it, plus a fillet of 5200 will seal the deal. If you are using wood this does make for unsealed penetrations, but you could put sealant in the pre-drilled holes. I was tempted to leave the bottom of the cover open so things could drain, but I think I will try for total coverage of sealant instead. That's my plan, and I'll document it elsewhere, but I thought it might give you some options.
Ron
BTW, you have some awesome fabrication skills.