Who builds his base in a valley anyway, in a melee round? :P

I'd say it's your job to make sure your base is protected appropriately against rain, if you know that there is rain in the scenario. Whether there is is a decision of the scenario designer. You are right that the amount of rain in Clonk is not realistic; but it makes the game more fun to play (to me, for certain rounds, at least), and this is what a game should be about. I'm just worried that rain might have much fewer impact on gameplay with your idea, and it becomes a visual effect only. This can certainly be nice for some rounds (esp. ones where you would disable rain completely with the current system). So maybe it should be up to the scenario designer to choose. But then again, newcomers might be confused because rain persists in some scenarios but not in others...