It's a known issue within Ford with a service bulletin for it. Find another dealer and make sure it's not in any more rain. It's not a quick job to repair and replace the necessary parts.
There is no ability to have the vehicle auto lock. I'm not sure where you heard the 2016 will have a different transmission but it's incorrect. The 21" wheels come with all-season tires with the option of getting summer only tires.
I keep meaning to look for one but always forget. The one from my Flex is too short, I need one about 36" tall. I like the accordion style as they can be folded up.
If you go with 3M tint, use their 25% to match the rears. Normally I go with 20% as factory rear tint is 18% but the tint place I always use told me 3M 25% is the closest to factory there is. He was right, looks like a perfect match.
Both the seat cushion and back portion are heated and cooled. It's mearly the design that makes the seat backs not as effective in getting as cool. It's difficult to get any significant amount of air into the seat back portion for the fans to blow. The seat cushion however is completly open underneath so it gets all the air it can handle. It's similar in other Ford models where the back does not feel as cool. My '13 Flex was the same way. I do agree that the seat bottom does get cold really quickly and needs to be turned down.
I believe I have the same exact problem. Mine is more of a slight tick coming from the back seat when I hit bumps in the road. This is in addition to the moonroof rattle while its fully open.