It might well do what you want - you're looking for "visual representation of relationship structures with notes attached to nodes"; Tinderbox is a program for organizing notes in a graphical fashion using nodes with arbitrarily definable relationships.
The emphasis / direction of coming at the problem is a bit different, but I'm positive that 80-90% of what you need is there, and suspect there's a reasonable chance that 100% of what you need is there. (I'm less confident about the bonus points, but perhaps? I found this page on exporting HTML5 articles from Tinderbox content, which isn't exactly what you're looking for, but suggests it might not be impossible.)
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It might well do what you want - you're looking for "visual representation of relationship structures with notes attached to nodes"; Tinderbox is a program for organizing notes in a graphical fashion using nodes with arbitrarily definable relationships.
The emphasis / direction of coming at the problem is a bit different, but I'm positive that 80-90% of what you need is there, and suspect there's a reasonable chance that 100% of what you need is there. (I'm less confident about the bonus points, but perhaps? I found this page on exporting HTML5 articles from Tinderbox content, which isn't exactly what you're looking for, but suggests it might not be impossible.)