A key element of xNode is backwards compatability all the way back to 5.3. This means UIElements is not an option. I also do not have the time to rewrite the entire framework to work with this new system. However, don't let this stop you from making your own fork which builds on UIElements. I'll even link to it if you do.

The best way to go about it is to create the graph in the scene instead of as an asset. You can do this by attaching the SceneGraph component to any GameObject. Graphs created in the scene can reference objects within the scene. Unfortunately this does not work for prefabs.

Alternatively, you can implement some ID lookup system.

Node grouping has been attempted a few times but never in a fully satisfactory manner. It remains on the to-do list.