Hello Mark,
if you look into this thread - importing annotations and then auto-connect them using Natural Language toolkits would help a lot when working with academic papers.
To set the links manually is one way to go and would deliver a high quality for the structure you create. But the automatic linking gives an alternative way to look into your data and it is very, very quick. Maybe we could call it “suggested linking” and this would be a feature to promote Tinderbox (Obsidian needs a PlugIn for this feature) too 
I was using MarginNote to create my annotations in a PDF. Margin Note puts those notes on a map and links them into a kind of mind map. This was helpful when extracting the ideas found in the paper. I left MarginNote because of its closed architecture and because there is no way to export the annotations together with the PDF. But the idea of using a map view to structure the notes is what I miss now.
The nounList function isn’t perfect if there is no converting of the different forms a noun could have. Singular and plural forms should make no difference here. And the NLTagger seems to offer an easy implementation but this is just a wild guess.
Thanks and have a good time in London.
Detlef