When I first received my X-T1, the door worked just fine. Then I had my camera worked on for the dreaded light leak problem that affected a number of the early cameras, including mine. When I got it back, the door bows like the ones mentioned above. My current solution is to take a piece of black gaffers tape and tape it down, which works fairly well.
I have looked into a possible DIY solution and I am considering trimming the inner door seal on the bottom and see if that helps. I have owned several Nikons (D80, D300, D700) that have experienced similar problems with the exterior rubber coating apparently slipping, swelling, and not fitting over time, so this is not a problem exclusive to Fuji
As far as water resistance goes, I have already used the camera in its current condition through several downpours and have had no problems. Short of dunking the camera in water (which I would imagine would get in the works regardless of the condition of the side door seal), I don't see a problem.