Tufte CSS
edwardtufte.github.io
edwardtufte.github.io
The design really works best in landscape mode. Portrait "works" but the sidenotes interact with the main text and each other in annoying ways. This sometimes makes writing documents harder than it should be since I have to test the output in both Landscape and Portrait to make sure it doesn't look terrible.
This somewhat defeats my goal of having a nice clean markdown->styled html workflow. I often have to make small changes to get things looking OK.
That said, I am very happy with the overall look and functionality of the style.
[0] An example page: https://sheep.horse/2017/4/so_you_want_to_start_an_unpopular...
[0] https://et-jekyll.netlify.app/et-jekyll-theme/
Edit: I realize you are referring to "footnotes" and not margin/side notes, but I believe you could use the same method.
The first is to use Javascript to dynamically move the footnotes, or to hide them behind a dynamic interface. I've seen other sites use similar techniques. However, one of my original goals was to avoid JavaScript where possible and there are always some users who don't run js.
The second is just to include the footnotes and sidenotes twice in the document in different places and use css media queries to select between them. This wouldn't be a big deal since I am already generating the document from markdown anyway.
But the support is still less than the 95% or so of users that most people try to support, and there are still glitches and bugs with them. Given that you'll have issues with the new skip-ink stuff and probably will have to include fallbacks, why bother with the churn? Maybe in another few years...