If it says not to, I wouldn’t.
The parts should be water resistant? I would guess people building ignitions would do that for us. If not there are products like this:
As far as rocks go, maybe cut the face off an old flywheel cover and louvre the sides. Plenty of airflow, but keep big stuff out.
I trust the big external flywheel to do all that on my CDI Setup. Never really thought about the problems with an inner rotor before. Those are my initial ideas. Does it sound like a reasonable approach?