I agree with your supposition #1. In addition, storing the wheel outside down shortens the bolt required to hold the wheel down so there is less potential torque at the bobbin. Since it is made of aluminum, it would be easy to wallow it out. Also, having the wheel inside up (to change things up a little
) makes a convenient place to store the tool set and the jack if I remember correctly. I wouldn't think that they were overly concerned about the appearance of the inside of the wheel because of the toolkit and jack storage. Because the wheel does not lay flat and sits partially over the M/C area, the outside is protected from abrasion from the fiberglass floor.
As I remember the original method of holding the wheel down was a bolt through a large washer in the center hole of the wheel. If memory serves, and it may not, the washer was big enough to fit partially in the center hole because of a taper in the hole. In any case, I don't believe it went through a lug hole.
So to bolster and refresh my memory, I checked the TC owners' manual and it shows a completely different method to hold the wheel down. The picture shows a strap and a wedged shaped stop being used and the toolkit and jack under the wheel (see TC Spare). That does not comport with my memory at all. The picture shows a steel wheel so I thought that may have been reused from the S2 owners' manual but from the picture from the S2 manual (see s2 spare), it shows a situation more like I described from my memory on my TCS. Now I can't say that the method shown in the TC Spare picture was never used but it was definitely not used on my car.