Update: Today I picked up the X-T1 body with the new skin, door and 4-way controller replaced for a total of $48. Looks brand new and the door is nice and flat.
I suppose I could have complained to Fugi or asked for the manager before agreeing to the repair price, i think they gave me a break on the labor though because the skin and door were only $20. I choose to have the 4-way controller replaced but they told me upfront that in their opinion the difference was minimal and now that I have it: I agree. They really should have raised the 'touch buttons' a bit more. Actually I brought some SUGRU from the U.S to build up the buttons myself, but even though I kept it in my dry cabinet, the stuff was rock hard when I opened the package.
I am very mechanically inclined, I make a lot of my own accessories, camera straps, flash modifiers, flash arms, etc. So that and along with my dental background, it looked to me that the metal is too flat where it meets the rubber. If they would create a 'dovetail undercut' where the rubber meets the metal, it would create a 'mechanical lock' and that alone would really help prevent the rubber from peeling away from the body.
What they did comes with a 3 month warranty. As others have said, it is a mystery, I have thirty year old bodies and they never did anything like that.