At first brush the idea the Spelljamming would have little to no effect on so-called "groundling" cultures is absurd. The ability to rapidly move people and cargo from one part of a world to another would have a profound effect on commerce and warfare in a mideavil society. Furthermore, the ability to engage in aerial bombardment, or to deploy "paratroopers" would fundamentally alter the nature of warfare and result in a "fantasy" world that would have much the same socio-political dynamic as our own.
Even the argument that spelljamming vessels are rare and expensive doesn't do much to alter this argument. If nothing else it only serves to heighten the absurdity of "spelljamming nations." What that argument ignores is the power of governments to raise the capital necessary, or simply draft into service the mages involved in the production of helms.
The problem then is how to explain the nature of spelljamming in a way that is harmonius with the desire to limit or negate its impact on groundling cultures while preserving it as a means of providing a believable setting for fantastic adventures.
If one were to envision planets and stars floating in an "ether", one could envision sailing ships likewise plying the "ethereal seas" and sailing from place to place. To avoid the problems mentioned above, one has only to envision that planets and stars are "islands" in the ocean of ether and just as it is impossible for a mundane ship to sail through an island, it is likewise impossible for an ethership to sail through a planet (or its atmosphere as the case may be.) By imposing this rule, we have effectively created a "wall" that seperates the two cultures and explains the lack of impact on groundling culture presented by spelljammers.
But this does beg the question of how such ships could take off or land from planets, which is a staple of spelljamming adventures. This is answered by allowing ethereal "rivers", "bays", and "harbors" that do intrude into planetary bodies in precisely the same fashion as mundane rivers, bays, and harbors do with mundane islands. Such "rivers" could be rated for the largest size of ship they will allow to land, and can be placed wherever the DM might decide—both effectively create "prime real estate" that would be fought over in exactly the same way that good ports and trading points were in our own world's history. Also, since these rivers would more or less extend only straight up-and-down, you effectively neutralize the martial advantage conveyed by spelljammers, and the requisite impact on travel and trade within a planet.
A mage or priest sitting on a spelljamming helm will be able to detect a known river automatically, therefore follow it up or down just as normal and before. Rivers on unexplored worlds can be found by making a intelligence check at a penalty ascribed by the DM. Likewise even established worlds might have undiscovered rivers.
Etherivers and harbors might change over time, with old rivers "drying up" and new rivers forming. Locations of rivers might fluxuate with the location of ley lines, and may even be ley lines themselves, simply ones that move up and down instead of across. The ramifications of this are left as an exercise for the reader's imagination.
