Here's a pic of my alternator with the cover spaced out. This was an XSJohn tip. I have used this for the last 4 seasons and I'm sure it keeps the alternator at a cooler temp compared to a closed in alternator.
I don't know if rain would cause problems, but just to be on the safe side, I remove the spacers (I carry an allen key on the bike) and close up the cover when I'm in rain.
In July I made a 5 day trip in the mountains, and of course it rained on 3 of the days. I simply closed the cover on those 3 days.