Hi @BackseatPete! Are you able to build a complete reproducible example, or reprex, for this? It'll help us working out what's going wrong for you.
In particular, I'd love to see your YAML code put into a code block by fencing it with triple backticks. As it is, those options for css and includes look like they're right up against the start of their lines. As YAML relies on indentation to create its hierarchy of options, it's possible this is causing R Markdown to lose those options. This link demonstrates some ways of properly indenting options in YAML (the main rules are (a) do it, (b) be consistent, and (b) use spaces, not tabs):
https://docs.saltstack.com/en/latest/topics/troubleshooting/yaml_idiosyncrasies.html#indentation
Hope that helps! If not, try using our guide to building a reprex and we can start peeling this apart 