If i “set multiple points” in grasshopper from rhino (created with array command) its a flat list with 100 points.
If i create the same points with the same arrays in grasshopper i get a data structure.
If you use the Geometry Cache object you can bake and reference shapes while keeping their data layout.
However data created in Rhino without specific user data which describes layout is always flat. You can’t even rely on the order of objects to be what you think it should be. If you pick points one at a time you can control the order, but if you window select them they may appear in any order.
Referencing a large amount of data and organising it in GH can be cumbersome, difficult or even impossible. It usually involves some sorting and, as @Michael_Pryor said, things like partition, list item, or culling.
In my view the data management in grasshopper is just WOW and i get better and better.
In the specific use case i need the option to move points by hand “geometry cache” sounds like the right option.
I construct my trees via Attributes, allowing me to go back and forth. A number of plugins are available to do this; Human, Elefront, Heteroptera and others.
This requires elefront. Once baked the points can be moved and still referenced in via the same tree structure. Do note if you bake again the movements points will revert to the original grid, so plan accordingly.
As i mentioned in my first post i used already elefront and human (great stuff) and tested also geometry cache. All of them work great but only human with the reinstate node work in realtime all other solutions need a hit on the update button.