Rust was once a major problem for automobiles, which led to a very active rustproofing market. Remember "Ziebart"? Fortunately, manufacturers adopted methods and procedures that have made their metals much more rust resistant.
Very few cars have made it this far in life without some type of floor pan damage from rrust. After all, floor pans take a beating when driven in rain, mud, or especially on salty winter roads.
During exposure to water from rainfall, car washes, etc., water gets inside the door. Manufacturers make some very good efforts to keep water out of the doors, and they provide drains for water that makes its way past the rubber seals. When the drain holes get blocked, rust happens.
Rust around the front windshield and back glass occurs primarily due to water being wind-driven during travel. If leaves and other debris are allowed to collect, and not kept clean and drained, the debris will hold the moisture and accelerate rusting.
A few photos of the floor pans before, during, and after, top and bottom.
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