Seamless planet transition with correct positioning

I have a setup of a solar system at a scale small enough that Unity can handle, but not large enough that the planets are realistically big enough to land on. I have the planets setup with a sphere colider that acts as a faux atmosphere and as you pass through it you get loaded into a new scene with the planet at a more realistic size. Then the reverse can happen an you can fly back into the solar system, this all needs some fine tuning to avoid loading screens.

What I have been wondering, how would I go about detecting where I entered the atmosphere so that I can spawn the ship in the corresponding point in atmosphere. At the moment there is just a hard set 'Spawn point', so it doesn't matter which side of the planet I approach it from I get spawned back at that one point.