Many airheads appear to have the rear wheel out of alignment with the rear subframe /fender, but usually it is do to a tweaked subframe and/or fender. My 82 LS actually is a little bit like this with respect to the fender, but it is due to some of the mounting holes in the fender being a bit egged out.
I seem to recall that on my 88 R100RT that the rear wheel was actually a little bit out of line with the front wheel centerline, but I think it is intentionally that way - unfortunately I don't have any good pics available to show this. So, your issue might be a combination of photo angle/perspective, rear fender mounting hole tweaking, possibly tweaked rear subframe, and/or designed in offset - I *think*.