I'm not sure if this is polluting the purity of your original idea but I think the concept of a meta-level note that only exists within the graph traversal space and acts as a commentary on that traversal might be useful

Is there any upper limit on how big a note can be? Could there be some organic mechanism for splitting big notes into smaller units which then share a common theme? This comment isn't directly related to resizing a note's window I guess, but it made me think

Could one perhaps split the viewpane in order to follow multiple paths through a chain of ideas?