Sardar, that's good analysis. We don't get water tanker. Our water supply comes from the line (in KDA) and it's used for everything other than drinking and food. The house water tanks get cleaned annually.
The weather stripping, or the door rubber seals are good and no water gets inside the door after washing. I have confirmed it myself. The water gets inside the inner door from the window bottom trims/brushes that seal the window glass. I looked carefully and there is a very tiny gap at the edges, especially right above the door locking mechanism. That's why it showed visible rust in that area first.
Irrespective of that, water does get inside the door inner panel for all cars and that is why there are brain holes at the bottom of the inner door, which let's the water drain out. This is true for all cars. This drain hole can sometimes get clogged and must be reopened. Mine were already open.
Since this is by design for all cars, if there was proper rust prevention coats done at the factory before the paint, it would not happen. This is a purely quality control or cost saving issue.
The trunk lid is also aligned properly. No water gets inside the trunk through the rubber seals, but during washing, some water may get under the plastic trim and the bumper where it aligns with the body. Same is true for the area behind the tail lights. It's either bad design or, again, quality of body rust coating under the paint.
Internationally, civics last many many years without such issues. There's even 5-10 years rust warranty by different manufacturers. I would expect the car to eventually rust, but not this bad within 4 years.