I've had the same thing happen to the bottom of my doors too, and I'm just as finicky about keeping it clean up here in the snow/salt belt.
What I did was I went to my bodyshop of choice and I had them grind the rust and paint off, clean and prep the seams, and seal the fold with a type of silicone sealer before painting it over.
If you look on the older contiques, ('95 for example) you'll see that it came with a sealer in those folds from the factory. The newer ones(such as our '98's), had it de-contented.
This sealer obviously helps, because my grandfather's '95 Mystique has yet to form a single spot of rust at the bottom of his doors. Unlike every local '98 I've seen, of which all of them have started to bubble there.
