IRA you're very lucky, because the very first post of a rusted door photo that I remember was on a grey Crossfire from Arizona. I'm pretty sure it was posted even before Andrew's historic thread.
If the car never gets wet (by rain or car wash) that's about the only way from keeping water from getting trapped underneath the seal.
Your seal must fit extreamly well, (or you send your car to the dry cleaners)
Rimshot, the trough is part of the door, I don't think it's a replacable part.
I don't recommend doing it, but some people have actually removed the rubber seal at the bottom of the door. If my trough rusted away, I'd probably try it, since you're probably going to have to find some replacement doors anyway.