It could be rain rot but hard to tell. I am working with my colt now because he has rain rot. I posted a few days ago on this and got some suggestions which I have been trying.
First, I bathed him in an iodine medicated shampoo. Today I started with the TMG solution. Which I think I will use a couple of more days. It seemed to soften the areas more and made it easier to brush off the scaps. I had another horse that had it a little when I got her and it got well with just brushing but my colt has it worse so I am spending more time to try and get it cleared up.
Your horse does not appear to be over weight but not under weight either. You should be able to feel his ribs but they should not be real visible either. I would agree that some exercise would be beneficial but not because I see that there is any obvious problem with his weight.