Very interesting! Funny, the little things you don't think about.
First, thanks Rus for posting the link to the Spare Tire Mount page, which I discovered had a missing photo. Got that fixed, and then started thinking about the photo and drawing which showed two studs on the lower left side, at odds with a couple of illustrations in the Parts Manual. And then my Vibration Dampener page which had images showing the two studs in every one of the four possible positions!
I went to one of my go-to photos, showing an almost brand new '61 3B:

It happens to agree with the Parts Manual: two studs on the top right side. I wouldn't insist this is total proof of anything, because I'm quite willing to believe that workers on the assembly line might not always orient it the same way. But it does seem to suggest that this was the way Willys intended it. And you might be able to make an argument that this would provide the best support when the tire caught on a tree or something, but I wouldn't want to get into that argument.
Derek