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Oh, didnt finish the demo at the time of writing the comment, my hands were just itching to point that out) 
Now that I finishedthe demo, I think that dual type levels are technically still the same, if we make a big bounding box as one big node, right? N-blule2 connections are saved. (This is what I meant by mapping the graph onto a shape, we can map all the edges that touch the outside world on a single shape.) If we go completelety into nodes only territory, we can do the third version, where we have several connections going into the same node. 
   

This also handles the {x} and -x- patterns and 'hanging' nodes surprisingly well, color and number coded all edges and verticies. The 1, 3, 5 and 7 blobs on the middle and right image arent nodes, they are A into A connections. (That's what a hanging node technically is, it seperates A and A planes on the left image.) Conversion is much more neat if converted into a middle version, with an all encompassing outer shell, but the rightmost one is technically proper version to do this.

Would this whimsical nonsense work, or am I missing anything?

I think that's the proper way to go between a graph and its dual, so in theory it works. But for this game there are a couple problems. First, currently the game only allows simple graphs (no loops or parallel edges), so for example you could only have one N-3 connection in your first example.

Even if we'd allow non-simple graphs, the second challenge would be layouting. You might have to connect far away vertices (the N-3 connections go around the whole graph), so making the final graph clean could be difficult. I'm sure algorithms for this exist but sounds like a lot of work for this game.

So, cool idea but maybe it has to be a separate project :) Maybe a game where one graph shows some clues and the dual shows other clues and you have to switch between them to solve it.

(+1)

Haha, I understand that this is an engine limitatin, thanks for even entertaining a possibility of such an idea) I love dabbling in theoreticals