I have the same bike, same size rear tire but different shocks. I am running triumph rocket 3 rear shocks that have a heavier spring than my progressives. While they were set at #3 the nut cage did rub on the tire occasionally. I only got 20K out of the soft compound tire I had been using but it wore across the entire tread running at 41 psi. I have since changed to a 205/60/16 Sempiro GT radial I got from Discount tire that has a nice rounded profile, running at the same 41 lbs. It is a harder compound and should last me a lot longer than the previous tire. However, I did not do the nut cage mod and run the shocks on #5 and do not ride two up. If you are running two up I would recommend you do the nut cage mod. I had no problem with any rubbing on my 4000 mile trip to Inzane and on to Illinois and did run into some really rough roads. I was loaded pretty heavy though with a carry all rack attached to the hitch carrying about 100 lbs, fully packed cloth bags, a duffel bag, tent, sleeping bag, two mats (since I'm old). If you are actually bottoming out you might think about going to air shocks for the infinite adjustability.
As mentioned earlier the nut cage is for clearance, but if you tire is going far enough up into the fender it will rub somewhere.
