Mike, I can assure you that the stock...OEM seat on your bike can sit out in the rain for 40 days and 40 nights of rain, and it will not get moldy/mildew inside the seat. However, after 40 days and 40 nights of constant rain, the bike may be at the bottom of a newly formed lake.
Seriously, the seat will not get wet UNDER the cover.
However, IMHO, I would cover that bike that is sitting outswide in the rain all day while you are at work. Bring a plastic bag...stuff the wet cover inside it for the ride home, then hang it up to dry out overnight inside your garage.