I've figured it out. To make the inline footnote works, must put the footnotes in the "Footnotes" section. Here is the example:
I have the file: "HDN is the best.html"
<title>HDN is the best</title>
<h1>Best of HDN</h1>
<p><sup><a id='fs-1' ...
Kindle devices have the ability to receive books via a special email address. Each kindle has a unique address ending in kindle.com. You can use Calibre to send the books via email to your kindle through your own email address. However, if the end goal is to bypass Amazon entirely, this method would not suffice.
Before sending any books to your kindle email ...
I hadn't looked before so I did a little investigating. With Calibre 4.23 on Linux, I found that it's not exactly Calibre, it's the Reader.
I don't know why this Reader (it's a newly re-written reader, but I don't know if the old one did this) is modifying the epub meta-data. There is no reason to do so that I'm aware of as bookmarks and other reading ...