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.

xNode graphs are stored in ScriptableObjects, and since these do not exist in the scene, they can't reference scene objects. To work around this, you can pass gameobjects into the graph as you call it, or 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.