Thank you so much! I was able to remove all the whitespace it by putting
<div class="tocify-extend-page" data-unique="tocify-extend-page" style="height: 0;"></div>
at the bottom of my RMarkdown file -- it looks to overwrite whatever is produced by tocify.js. The page is more than long enough to scroll all of the TOC contents, but it's good to understand why that feature exists.
Really appreciate it, so happy to have this gone 