Magic changed dramatically with the introduction of Universal Magical Theory in the mid-sixties. So the Elemental/Nature Spirit divide was a huge mechanical and story issue until then. Virtually all other Traditions were seen as socio-religio-cultural expressions of the two dominant Traditions and they weren't functionally distinct until later as research progressed and made them different. Voodoo is also in the same group as Idolists, Druids, and the Path of the Wheel. Yeah, they existed, but ... (and there is a "but ..." to that). It also has the added catch of being a Possession-based Tradition that had eleven pages of Awakenings dedicated exclusively to its introduction (Of course now a lot of that can be cited to "See page xx, SRA/Street Magic" for a specific feature).
But as you note, Physical Adepts did exist in 2050. They just weren't added until The Grimoire. Likewise, the ways powers were introduced was often a matter of "this has been around for a while in very limited circumstances." Social Adepts especially were in a group of "No one realized they could do this until some serious research was done into the issue." Almost every major NPC who is a Social Adept has been one since before 2050.
Now Metamagic, on the other hand, was generally a matter of "No one knew this was possible ... Until now!" So if it was up to me (and it isn't, since I am not involved in the book) I'd limit them to Centering, Masking, Quickening, and Shielding. Dispelling was a Metamagic for a long time, but I'd just as soon not bother. SR4 is supposed to be easier, and that's just excess details.
But you make an important observation: This is a (mostly) setting book for SR4A, not SR1 Redux. Every hard or soft retcon that has remained canon in SR4A is probably expected by not a few people to be a part of this book. That said, if you are playing a Houngan in 2050 Seattle then the fact is that your PC is the ONLY Houngan in Seattle and that is going to make life hard as Hell for your PC. No one, including most of their own, understood that Social Adepts were anything more than really talented mundane Faces for another decade-plus. Many probably never developed or burned out their powers pursuing other paths. But at least they won't have to compete with people with Tailored or Cultured Pheromones.