After doing some reading, it seems like rain that hits the top of the WSM and trickles down, will go into the smoker instead of roll off the side (this is not a vent issue). If you look at how the top dome fits into the middle barrel, you can observe this. So that water accumulates into the bottom part. When you have trapped water, plus dark, plus oil/fat on walls, you get mold.
Options to reduce this are - store WSM out of elements; put a garbage bag over top when not in use; flip the middle barrel such that water doesn't want to go into smoker. None of them are that horrible, but it just adds a few more steps and you have to wait until after smoker cools down, so not as simple as an on/off switch. I was hoping that a new cover would help avoid this for me, but it didn't work.
I made some excellent pulled pork yesterday, but it rained last night, so I probably gotta do a full clean-out today. I think I'm gonna store the grate separate from the smoker until I can lick this mold prob.