Haha. Yes, about that. So when RPC adds a node to the project it's positioned in the center of the Node Network pane. I've gotten into the habit of moving the Node Network view to where I want the nodes to appear. Now RPC will still stack the nodes on top of each other, but they're a little easier to deal with, rather than stacking up on some part of the node network that you don't want them to be, like the Atmosphere group.
You mentioned you had 10 Crater nodes close to each other, but imagine you had 100. What a job that would be to unravel and reposition them. This is the type of situation that scripting is great for, i.e. repetitive tasks. I've already written a script that unravels selected nodes. I haven't released it to the public yet, but I use it all the time. I simply select the entire cluster of nodes that are stacked on top of each other and run the script. It basically repositions the nodes vertically so they're not on top of each other. It's then much easier to move the entire group of crater nodes where you want in the node network view. That's how I got the "nice" look in the example images.
As soon as I'm done with the current scripting project we're working on, I'll get a version of the unraveling script posted so you can use it.
I've been thinking about how to incorporate what the unraveling script is doing, so that it can be added to other scripts like a function call. That way the nodes would be better aligned to begin with.
Just so you know, the node connections are correct; the nodes are just stacked on top of each other.