Personally, I've found using a cover can sometimes affect the heat - this appears to have caused slight marks (as if caused by smoke or scorching) in between some of the keys.
I'm not using the cover at the moment to test this and your right it does appear to be a bit warmer with the cover on. However the risk to my MB from my juice wielding toddler
The marks that form are dirt. A moist cotton bud will clean it off and if you don't mind then saliva is a very good cleaning agent (again on a cotton bud).