Success!
OK, I think I was missing your point, Bookworm_girl. I have now found that I can export my notes and markups in the context of the page if I use the pen feature. When I highlight it only shows the section highlighted, but when I use the pen, it gives me a marked up image of the whole page along with underlines and notes. Super cool, and sufficient for what I need to do.
For me, the default markup will be underlines and bookmarks then. Highlighting is OK for making a reference, but not a contextual one.
Thanks again, and apologies for being dense.
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