I come with fantastic news!!
I know what I need to do now and I know it can be done with ease as a result. I have gotten the base building app to recognise the instances created by Blenders geonode tool.
The next step is refinement, getting the best effect with the least amount of spheres or even experimenting with other objects for different segments.
Whats the base part limit for a base again? Current raw attempt was actually smaller than I was expecting, only 4,700 spheres (before clean up, which I also intend to do once I’ve refined the geonode instancing a bit). I was worried I was generating 10,000 spheres in blender at first '^_ ^
DJmonkey, who makes the plugin/app, helped me over the finish line too, by letting me know which attributes on an object in blender, were important for the export to NMS button to recognise them too. I owe that person a steam purchase of their game I think 
Edit:
Have it reduced to 1900 parts, going to test it in a different system to see if it doesnt tank performance or anything weird before I even think about putting it in our system for the Artemis launch.
Its hard to know how the colours will look from the app but I’m hoping for some happy accidents.
Edit:
Looks good on PC at low/med mix settings with zero effect on performance
