Yes as issue in Github.
For this one, the use case is bookdown but the feature is in Rmarkdown where _output.yml is from. I would suggest there.
The impact can be non negligeable for this and output can already be pass to render_book as object in argument of the function. Maybe a function to help transform an output format stored in yaml to an object would be enough in your case
render_book("index.Rmd", output_format = as_output_format("my_output.yml"))
This is a different approach but could be easier to implement... We will see what they say.
Doing what you do (renaming to activate), is also a good way. You can use a Makefile or other workflow tool (like drake R package) to help automate this. Or just a wrapper aroung render_book 
render_book_with_yaml_output <- function(input, yaml_file, ...) {
stopifnot(file.exists(yaml_file))
if (saved <- file.exists("_output.yml")) {
file.copy('_output.yml', '_output.yml.save')
unlink('_output.yml')
}
file.copy(yaml_file, "_output.yml")
on.exit({
unlink("_output.yml")
if (saved) {
file.copy('_output.yml.save', '_output.yml')
unlink("_ouput.yml.save")
}
})
bookdown::render_book(input = input, ...)
}
Somethink like that...