If you can't/don't want to mess around with a masking area - I've taken the non-lazy route and doubled up my layers and added some events that move objects/characters/etc between the various layers to be in front or behind the weather layer. It wasn't my ideal solution because it seemed like over-complication and double handling of objects - but it's working now and I should stop being so lazy!

Cheers for all your effort - the rain and lighting effects look super!
~Sol