Removing center vent completely

You could use a piece of 1/4 plexi glass or plastic as you mentioned and just Dicor it. Eternabond is great but not needed. $8.00 tube of Dicor self leveling will work just fine. Its like sealing around anything else up there and its easy to remove.

Some very nice skylights with shades are offered on a few classy rigs. I think they are more popular in Australia, but are not unheard of in the USA. I think they can be installed with great reliability.

For a flat roof motor home, I wonder if a domestic (regular house) skylight would work just as well, maybe even better, maybe lower cost too. Certainly there are many choices & sizes at Home Depot and Lowes, some with integrated shades and good thermal properties. Just maybe you could find the right one that opens with a bug screen. Aerodynamics of the rig may work well in regards to concern over wind-driven rain. If not, later add a wind deflector in front of the skylight.

Here are a few examples of skylights in motor homes.

Check out the RV skylight covers. You might find one to fit most if not all of the opening and not have to bugger up a homemade cover.
Then you'd have some extra light in the MH also.

Just go to any local camping store. They have a HUGE book of just about any part you need to order for an RV.

Or just buy a MaxxAir cover that should fit it too. Then you'd have the option of using it as a vent with or without a fan.

IMHO even if you think you are going to keep this RV forever. It would be easier to sell if you had a manf vent cover over the opening.

There are a couple of reasons I want to just close it off. One is that the aluminum cross beam broke and I had to reinforce it with a metal beam. I don't know if the weight of the air conditioner bouncing around did it, or my butt on the roof, but until I took it apart and repaired it, I had a tremendous water leak that caused quite a bit of damage.I am hoping that closing it off will help with the prevention of another leak. Maybe this will explain it a little better thanks

What you propose probably would work, but why not fill the hole with the vent you removed. I can't imagine doing away with a vent. If it the summertime heat that you are concerned with, you can get a foam pillow from Camping World that fits perfect. Keeps the heat and heavens forbid, the Cold out.

That would be a real PIA in my rig - would have to try and find something to blend in with the existing interior ceiling and I suspect it would always look like a "patch" possibly impacting resale. Have you considered putting in a replacement vent and leaving it closed - if light etc is an issue you can always buy a solid metal lid for the vent.