couldn't you use a fx trigger to simulate the transition between the two. So as you approach the next area us a fx trigger to start the rain at a lighter value, and as you got closer up it. I know it's not ideal cause having a blend between the two would be wonderful, don't get me wrong.
But another thing to think on is making our own rain effect, like cooper's tutorial for snow, and then utilize the fact it's locked onto the character, then use a trigger to turn on and off the fx. based on any condition you needed. Might work better than trying to blend between everything.
I do though so often wish there was a way to blend a different seamless link area's scheme with the current area's scheme, would make things much easier. I mean there is always some way to trick the appearance, but at times it's just a pain.
Heck last night I spent 30 minutes screwing with a light, just to get a transition from an above ground area, to a cave system which needed to lose all light. so had to try and make a transition area where the light between was blended enough. Or if it was in same area, I just move a slider around, and done. lol