Very odd.
I can't tell you why this was done. But I will tell you why you need to fix this. The second picture is what concerns me. There are several places where someone has drilled through the frame. Fortunately, This is on the back of the trailer, where the load is not so high. But each of those holes are weak points and could lead to cracks in the frame. The ones that are from one side of the frame to the other are especially confusing. Is there something bolted to the inside of that frame rail, or is is just a bolt?
Since you don't have a use for the tin, or the extra bolts, I would remove the body from the frame, remove the tin, close up the holes in the fibreglass, (this is a good thread on the subject:
https://www.fiberglassrv.com/forums/...ass-52498.html) then take the frame to a trailer shop and have them remove any remaining, unnecessary bolts and weld the holes closed. Basically a rebuild.
Mud flaps are not a bad idea, but extra holes are a bad idea. I would just remove the extra bolts and glass the holes closed.