Codge - Mr Copes word of the year and what a fantastic word it is too!
Reading the difference in opinion between Ormplus and Mobbster, Smallboy is now probably wishing the question was never asked. Don't worry about it, that's what forums are all about. The banter can get a bit heated at times but at the end of the day we are all individuals with our own opinions and express them we shall.
Even if you're Dr Who and have been fixing things with your sonic screwdriver for over 900 years someone will disagree with you - guaranteed. What a boring world it would be if we all agreed with each other eh?
So you now have choices (IMO);
Leave the cover as it is and remove it regularly and let it all dry out.
Drill a hole in the bottom as a drain (also works as an inlet with the vacuum effect mentioned earlier.
Only use WD40 if you regularly remove the flywheel for cleaning. An electrical specific protector like Copey mentioned is the best bet.
Drill a hole and fit a breather tube up the frame (seen this done on quite a few bikes)
Try sealing the cover in place with something (codge?) (Sometimes works, sometimes doesn't).
Personally, I do the regular removal, blow out with an air line and spray with ipone protector, leave cover off until thoroughly dry - school of maintenance. Other opinions may vary - always read the label.
GJ