OK. You guys are quick. The plate in the 3rd picture is confirmed to be for a stern light. Googled it and found a picture. I will go with the flag pole tube as well.
thing is that I bought these for a catamaran
and the rails will actually be rotated so the short end is on the stern and the long side will be along the sides. I don't intend on using the stern light plate, but maybe I can repurpose it for something else. The flag tube will be on the port side, so there again, I am not likely to use it for that either. I will buy a plastic cap for it.