I'm not sure if the "layer" files will change the weather pattern or not, but one way to think of the settings for weather in those files is as a "standard weather", or "default" setting, so that whatever the game engine generates is what you get. The last mission file loaded is the one that you would put weather changes in, such as "Patrol Attu Island 01.mis", and in those Patrol Objective files is where I'll see some weather changes, though I have not "proven" this as so, especially in light of the fact that sometimes the mission still starts with clear weather...
- but missions into the North Sea, or the Bering Sea, you would want inclement weather more often than not... As to the "big picture" of controlling it in the game, I have no idea myself.
