Well, if he's right, you have to make the rain able to get trough bedrock (and nether-rack?) if your world is a neather and the bedrock's position isn'nt 0-5 (the bedrock which is on the bottom of the map).
how about almost impossible. It is impossible I believe to make rain go through object or change where it rains from, so I personally think this is not hard, but nearly impossible, I mean it can rain, but it will never hit below, and no code that exists yet could change that. That is something that maybe could be in the next bukkit is being able to set the location of the weather.