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I think this is caused by the lines being drawn with Godot draw calls but the nodes are then actual GUI controls. So the positions versus when the rendering update happens aren't exact so when panning with the mouse the nodes and lines are slightly out of sync with each other and the screen looks jiggly / fluid / non-rigid. I think it would be nice to find a fix.
I tried really quickly making the node positions apply only after a graphics draw but that doesn't help with the problem (and introduced cases where sometimes the positions got really stuck and out of sync).