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Maybe chat to the dev of https://github.com/ahrm/sioyek about adding this as a feature. It's probably the closest pdf viewer I can think of that might do something like this in the future.
You can use Logseq to highlight text in pdf and make notes in markdown, see Logseq PDF hightlights. It's very much a note taking app first though and not really a document viewer.
Possibly: Org-noter and/or PDF Tools.
Possibly: Org-noter and/or PDF Tools.