I had the same issue with the alternate prime planes being within spheres on the same plane, but since I really like the crystal sphere concept, I just went with it.
Really, though, you can combine the two ideas just fine. Each alternate prime plane is a system within a crystal sphere that floats within the astral. Ships sail to the edge, exit one of the exits in the crystal sphere and enter the astral that way. You're only really losing the phlogiston that way and everything else fits together nicely.