Rain doesn't affect Endermen and monsters still burn during storms. I think that is happening as its not vanilla rain.
That vanilla rain/weather2 rain issue is causing a lot of compatibility issues with minecraft+ other mods

I think this issue should be reopened. One thing I love about this mod is localized weather and I think it would make sense to patch vanilla mobs at the very least to fix this issue. Having to give up one of the central features of the mod to have compatibility with vanilla features feels like it defeats the purpose.

Set "storms when" to global overcast for better compatibility.