Hi, welcome!
Everything that rmarkdown does goes through knitr and pandoc. In the yaml, you can specify a fair amount of LaTeX arguments, I've gone as far as including Haskell parsers to get LaTeX tables right.
You'll notice at the end of knit the command string that puts the whole chain together:
/usr/local/bin/pandoc +RTS -K512m -RTS tcase.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output tcase.tex --template /Library/Frameworks/R.framework/Versions/3.6/Resources/library/tufte/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex --highlight-style pygments --pdf-engine pdflatex --variable 'documentclass:tufte-handout'
So, I fear, what you will have to do is to add a LaTeX document class where /Library/Frameworks/R.framework/Versions/3.6/Resources/library/tufte/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex --highlight-style pygments --pdf-engine pdflatex --variable 'documentclass:tufte-handout appears.
That, I think is the sound position for a template you expect to use a lot. I find it a lot easier to write scripts using bash tools or Python to batch correct the offending option you found if I only expect to be processing this format a few dozen times. Writing LaTeX templates is not what I want to spend my time doing if possible.