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Bondo is best kept to under 1/8" thick, as the thicker you make it, the more it tends to crack with age due to differential heating and shrinking compared to the material under it. However, for a year or two, it does just fine up to about a 1/4" in my experience.
Expansive foam can be hard to control, as it tends to grow for an hour after you spray it in. It's also sensitive to UV light and tends to degrade if not protected and I'm not sure how it will stand up to spray paint (does fine with household paint and it seems to protect it).
As for weather stripping, go to several stores and look at options. There is magnetic stuff (used on some steel doors and also used for sealing refrigerators) but it doesn't conform to curves very well. There are also different density foams. Most are not designed to stop water; they're designed to stop airflow. However, I suspect the more dense stuff will do both pretty well. You may want to go with two strips side by side if you can.
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