TDK,
Just aquired a flaky Supra myself and I am wrestling with the same dilemma. I saw one sell on eBay (or Reverb) in the last few days that was painted nicely with a hammered look paint. It was a mustard brown which was kinda fugly, but the paint looked good. It went for a price that was only a bit less than what a flaky example should bring.
I like your train of thought to wrap it with something, then it could be put back to original if needed. Someone needs to invent a shrink wrap specifically for Supra shells. They do make clear shrink wrap bags for things like Easter baskets. I wonder if you could use a strip cut from one of those, then it would be seamless.
I was just going to slap mine back together and deal with the flakes, but maybe I'll give the wrap idea a try.
AL