There's your problem right there then. That tile you set to X is essentially the blank space, which all three of your layers use. What you want to do is set that to passable, and set the one next to it to impassable. Then, fill the outside of the first layer with that impassable tile (fill in where there would be wall). You can double check that you've got the right tile in the right spaces by temporarily setting the autotile to a graphic, so that you can actually see where you're putting down the tiles.
Also, the weather is going to continue endlessly unless you turn it off at some point. This means you need to check your events in the map you're transitioning to that you don't want the weather to continue on. Either your event that's supposed to turn it off is not running properly, or you have another event set that's actually turning it back on. My guess is moreso the former. All you need is a parallel process that sets the weather back to none, and then you erase the event.