Maybe so it wouldn't get lost during shipment? I really can't believe that you've owned the mower this long without removing the cover. Whenever I get a piece of equipment, new or used, I always go through it completely, just to make sure fluid levels are right, belts are tight enough, etc, before it's ever hitched to the tractor. Too many horror stories out there of people buying a new bush hog, putting it to use and finding that the store didn't fill the gear box until it locked up, etc.
I agree that everything should be right on new equipment when you buy it, but you're dealing with people and people mess up, intentionally or not, so I always do the "trust but verify thing"