This topic has been in my thoughts for a couple weeks now (and really bugging me). I got my "new" '05 a month or so ago and upon inspecting the channel at the bottom of the doors last week, I found some rust in that "overlapped" area on both doors. Regardless of what people are saying, this is not going to be an easy area to fix because of the lapped seam and the 1/2" area where there is no paint in between these welded/lapped parts. On my car, the seam is sealed on the bottom side from the factory with some type of seam sealer (helps hold the water in there...?!?). There is going to be moisture trapped between the overlapped parts unless you take a blow dryer or heat gun and dry out that area completely for a while prior to applying paint, POR-15, or some kind of sealer. I really like using POR-15 on rusted parts, but I believe that it's not a good thing to use over existing paint (the original paint will eventually bubble if there is any water/moisture getting in there or already there). At that point, the POR-15 is actually helping seal the water in instead of out. (POR-15 is only as good as the surface or paint it's being applied to, so over existing paint, it's not doing a whole lot).
I dried out the seam area with a light application of the heat gun for an hour or so. I spray painted the seam where it was necessary because of bare metal. I then applied 2 coats of auto body undercoat sealer with a brush over the seam area and any place else where the edges were unsealed. After and hour or so of drying, I re-inserted the rubber molding. I'm hoping that the flexible body sealer will do a good job of sealing this area from moisture, but won't know for sure until next spring when I check it again. Good luck you guys and thanks for posting this issue in the first place. A proven/quality repair could save more than a few doors...