Alas, in spite of my desire to do this upgrade to my 12.5K JAYCO, it likely will not happen. I asked a service manager at a reputable trailer repair shop his thoughts on making the change. My wife was standing right there, because it was her idea to ask a "pro". I think his answer was a little outdated, but it has settled the discussion in our house. He said that sooner or later every brake controller will break down and you can't find anyone to work on aftermarket conversions.
I hope I don't find anyone to say that replacing a dirty old rubber roof and its inherent black streaks with a "rhino liner"-type roof is a bad idea. That would shoot another good idea in the head, in the interest of frugality.