Suitable diagram for sparsely and densely populated nodes in a table

no, those are just HTML Elements and the gojs diagram is being drawn on top of the HTML Table layout. So only completely white rectangles with border are gojs nodes.

Hmmm, I just tried this, and it works as I would have expected.

Can you try to create the following layout and see what happens?

Earlier I had not included making sure the fromSpot and toSpot were limited to particular sides, depending on “openness”, but now I have done that too, and I still do not see any problem.

So I do not see how what I have tried is different from what you have.