I had my 2013 Mustang GT in commercial storage for two years inside one of those balloon domes, and you couldn't believe how dirty the engine compartment looked when I took the car out. As alluded to by other posters, it's probably due to the hood vents which started in 2013. Then Ford started making them smaller on the 2015s and up.
On my car, there was bad water spotting around the engine compartment too, which was really difficult to remove even though we don't have very hard water here in Hawaii. At first I thought the storage employees were driving the car around, but couldn't be due to the mileage (and the spider webs in the undercarriage), so I guess they were washing the car once a month as they advertised. It was really a hassle getting the engine compartment clean again due to all the nooks and crannies where you can only get half a hand in, or a couple of fingers, so good luck!