I have used bike covers for years. Both in a garage and outside of a garage.
I have lived near the ocean with high humidity and in the desert of the US southwest with very low humidity.
I have not noticed any ill effects to my motorcycles.
I am certainly not saying that you won't have ill effects. I can see how warm trapped air in a motorcycle cover could possibly lead to condensation. That being said perhaps an experiment over the weekend is in order where you could get the bike good and hot and put the cover on and periodically check.
My opinion, after seeing dew on my bike frequently when I lived by the ocean, dew shouldn't hurt the vehicle. I'm a bit of a vehicle abuser and have driven dirt bikes into lakes, just cuz, in the past. Mind you, I'm not proud of that, but so long as I flipped it over and got the water out of the intake they always started up and were able to beaten up further afterward.
I know this is very subjective and not founded in facts. I don't even have citations. So let the downvoting begin!
Cheers, I hope this helpful.