The CDC does define a cruise ship as a congregating setting, so the default lens is that for a crowd. I agree It's very much possible to spread people out at the islands and do the pods as you suggest. The CDC would still have to come up with rules specific to such private islands - much like it has done for the shore excursions. It's all not very different from the cruise line being asked to enforce masks and social distancing on the entire ship even though we can argue that the top deck is 'outdoors'.
If, by November, the order is significantly modified anyways, this requirement may just be a part of what they are calling a phased restart. Walk before run, you know.