R_J_K75
Legend
I suspect they realize this was a mistake and are working on ways to undo it for 5e. Although I honestly think they overthink trying to create continuity from edition to edition. Sometimes simply hand-waving something away and pretending it didn't happen is the best option.
Yeah. Best thing they could do is just give the pertinent rules of how, if and where the setting interacts with the planes, and prime material plane(s) and make it its own standalone setting with whatever special mechanics it needs. The only exceptions I could think of off the top of my head where Spelljamming might be affected or voided is Dark Sun, Eberron and Ravenloft. Even if that's the case a few sentences can solve that problem with something to the effect, "these planes are not accessible by Spelljammers".