If we're going to have an x / y coordinate setting waypoint system to use from the system map...
(Which might change completely, to a more "orrery" based system, hopefully because, rumours...)
We're also going to need a way to plot a z axis for height above (or below) the surface or orbital cruise line in the case of gas giants as well. Otherwise, it's not going to work for setting a waypoint suspended in the atmosphere.
We sort of have this problem already, you can't see coords when you're sitting in a mining ring for example and the whole thing is made more complex because clouds and other stuff that's not fixed to a point on the surface relative to the polar axis isn't going to use a typical x / y coordinate anyway and what about pole flipping and other peculiarities like obliquity?
(Earth's current 23 degree tilt is not static either, just FYI. See "Milankovitch" cycles)
How about a system where we can set an x / y / z coordinate based on the centre of the body we're looking at and some kind of overlay that provides an arbitrary line graphic ball so we can click on the centre of any object then drag / steer the cursor to any point below, on or above the surface geology / liquid / cloud top / ring?
Tricky to program I'd say but due to the massive variability of celestial objects, any system will need to work regardless of surface features on the rocky and icy moons we're currently able to land on.
[Edit: Confession - only read the OP, throw tomatoes if you must

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