In practice, I've had better results focusing on graph creation and connections through the Graph API rather than trying to automate layout. If automatic arrangement is critical, you may need to rely on manual arrangement or a custom positioning system using node coordinates (if available in your node space implementation).
Resources:
Maxon SDK forum discussion: https://developers.maxon.net/forum/topic/14311/python-callcommands-geometry dash lite-are-not-executed-when-using-nodes/6