Rain isn't what stops the express transportation from running. It's lightning within the same sort of radius that shuts down the Friendship boats and all the outdoor attractions. The reason is that the Guest Relations CMs at the check-in locations that escort guests on and off stage are pulled indoors for their own safety when the "lightning call" is issued.
If guests are on a bus en route to a park when the GR CMs are pulled inside, they have to be dropped off "on stage" at the regular stops because no one will be at the backstage location to escort them.
I think someone here has mentioned the entire system shuts down with the lightning call. Do you know if this is true? If there is a storm over AK, why would say the DHS to EPCOT hop need to shut down.
We've all heard stories of pouring rain in MK and bright sunshine in DHS.