I can see what you mean, both cases have their drawbacks of being a little time consuming. I thought about this a bit and had an idea of using JavaScript to find links on the page and generating a footnote from those links:
In this CodePen I’m using JavaScript to locate any link in my main content that contains “fn” and converting them into a footnote. Whatever link is applied to the “fn” text is then generated at the bottom in a footnotes section, just like in the markdown version.
With this creating footnotes is as straightforward as creating a regular link 
. I’ve also written the code in such a way that you can choose what text to be in the link, so instead it could be “more info” or “details”. Hope you find this useful 