This is great! I love when a comment expands the original writing. Numbering for some clarity...
1) When citing a book -- you can do either, but I think just linking in the text is what I see in the Medium publications. I try to use the Medium inhouse pubs as a guide to how they like stuff done here.
2) On style guides, I think personal preference probably wins.
3) On learning from a course, if it's online or there's anything "to" link to, I'd just do that. It's not always possible -- I took a marketing course 20 years ago and even when I mention it, there's nothing to cite other than a mention out of acknowledgement. You know?
4) On the story from a book -- I'd just reference the book with a link. While credit to a source is respectful, I don't think we need to relay how we came upon a book. We'd end up with so much besides the point, we'd lose reader focus.
5) With the double reference, honestly I'd just link the book as the citation and not worry about citing the way we would in a college paper.
Thanks for reading and adding to my post, too. :)