I really enjoy these notebooks so far and can't wait to experiment with them. Super minor issue: this is probably a dated approach, but you can eliminate trailing whitespace from your knitted .html files by adding the below html code to the final line of the .Rmd file:
<div class="tocify-extend-page" data-unique="tocify-extend-page" style="height: 0;"></div>
I think there might even be a short R function now to do so, but this was my goto for years to keep notebook scrolling snappy and tight.