I think there is still a misunderstanding with some people as to what exactly the problem is, or how it is caused.
As long as the factory drains in the door are open, I don't think you have to remove the black plugs at the very bottom of the door. I don't think the doors themselves are holding any water. If they were, you would be able to hear the water sloshing around in the door every time you open it. Or see tell-tale signs of your doors "weeping" on your rocker panel.
What causes the rust to actually begin is water that is retained by the weather strip is being trapped against the small vertical section at the back of the trough that holds the weather strip. Unfortunately, this is exactly where two pieces of metal "overlap", and on the very edge of that overlapped metal is where the rust seems to start. Since it is a continuous seam, it's very likely that moisture seeps down in between these two pieces of overlapped metal, and eventually comes in contact with metal that has no or very little paint or primer, and the rust process begins to spread under the metal that is coated.
The real culprit is that exposed seam, and of course the fact that the weather-stripping shouldn't be retaining water in any location either.
If you can successfully "seal" that seam (well actually the entire gutter) then any water that lays there will be harmless. That's why I'm going to probably drill holes in the bottom of the trough to encourage and facilitate water drainage. Deciding just exactly what kind of paint sealant I'm going to use is the question.