The only drawback from previously marketing EotE and AoR as "standalone" is they now need to re-market all three books as the "complete trilogy", and make it clear that cross-pollination of careers and specs are encouraged.
I agree, and i think that they should add a page which suggest doing that and gives some examples of possible careers that mixes the classes and the specs, a bit like they did in Far Horizon (that was one of the best parts of the book: explicit path to build different careers).
I also think that the "force sensitive variations" of the Edge/Age careers are useful beyond the stand alone part: they add flavor and allow you to fully implement certain character concepts better than before (IMO the Gand Findsman should be built as Seeker:hunter/fringer rather than the more convoluted Explorer:scout/fringer/Force Sensitve)
They kind of already do this. There is a few pages on combining Age and Edge. and i suspect the same will be true for F&D