The cover on our RT has a section that sits in front of the rear wheel arch. The wing-nut is screwed into the wheel arch through a hole in the section. This prevents the cover from separating from the van. However, we also have a handle that is spring loaded and pulls down to engage the bottom edge of the cover against the van body. The velcro strip works, but I am not sure how well. If you were to fasten the bottom edge of your cover to the underside of the battery tray, on a removable basis, the cover would not come off, inadvertently.
I did a lot of experimenting to eliminate rattles. One was to put a strip of electrical tape along the edge of the upper and lower metal flanges. Another was to put a strip of electrical tape on the body of the van at the level of the top edge of the cover. Another was to wrap all of the door latch bars with electrical tape to minimize rattle and play. The worst offender turned out to be the spare tire vertical shaft which could be cured by lubrication for a short while. The solution was to put shims on either side at the hinge bolt.