I created
~/.config/rstudio/templates
and saved a copy of the default notebook.Rmd there with a change to the title to show that it had come from that location, rather than the default path
/Applications/RStudio.app/Contents/Resources/app/resources/templates
which was created by the installation of RStudio.app (I didn't do that manually).
Creating a new notebook uses the template from ~/.config/rstudio/templates. Opening an existing notebook shows whatever template it was created with.
Any template applied by the new notebook file option has to be named notebook.rmd; notebook_osx.Rmd won't work.