Thanks for sharing theses examples. I'll look into it closer. There is a WIP PR to relax as we could this index.Rmd constraint
I'll see how this works with your use case.
you example helped me to understand that you are using bookdown to create a website which is not necessarly a book structure, and even using bookdown to create a blog like structure.
I just wanted to add that design of bookdown project and features are really for book structure, i.e HTML websites which are mainly one big document splitted in several files as chapters or sections. In the R Markdown ecosystem, we have other tools like distill or blogdown which are more suited for project which are posts / articles that leave together in the same website and that can be render independently of each other. This is a big difference as for example, bookdown is no made so that a single Rmd file of the project can be rendered independently of other files. It is really made to render the whole book.
I'll see what I can do restore the old behavior without reverting some necessary fix for Book project.