The factory itself doesn't fit them that way and yours isn't fitted that way either. There is no way the interior tub will fit with the body a quarter inch lower. Also that would put all the weight of the body on the bolts instead of the chassis.I checked with Fran, and according to him, the order is as stated in the manual, which is "... from the bottom, skirt, body, aluminum chassis extensions", with the body pulled a bit to stretch over the extensions. That makes the extensions the top part of the sandwich, and allows the two fiberglass pieces (the body and the skirt) to fit perfectly together.
You can mount them as Allan suggests as well, and that has the benefit of not having to pull the body a bit wider to fit over the chassis extensions, which makes it easier to remove and re-install the body. The disadvantage of that approach is that the extensions aren't at the top of the sandwich, which perhaps doesn't look as good.
Either way can work, but the order in the manual is the official method from the factory.