Well, come to think of it, I think the idea of TN technology is that your ships move through space as if through water. There's no reason to assume this would work in interplanetary space but not work in the atmosphere (except for friction, drag, etc). So presumably a TN ship can take off from a planetary shipyard under its own power. This also explains how 40,000 ton freighters can drop things off and pick things up from a planet without a spaceport... they simply land and take off.
However, this still does not explain artificial gravity in a ship. The ship itself can move in defiance of gravity, but that doesn't mean the same tech can create artificial gravity to pull other objects toward it (like pulling the crew toward the floor). On the other hand, the game has tractor beams which seem to do just that. Perhaps tractor beam tech is what you're looking for?
Also note that TN ships do seem to be affected by black holes but I haven't seen one yet so I'm not sure how they are affected.