Do you have any objections if the software can detect the hyperlinks and make them fill the circle if it's a detail callout? We could also make so hovering over it shows a preview?

Typically when a PDF imports, it looks like this:

Or This:

Also, maybe we lighten the color a little (as in the first image above) or make them transparent altogether?
Some users feel they stand out too much, but we want users to know if the software has detected them.