Hi,
I did not even know this was a feature. That you could put _output.yaml in content/post to share options. It was a nice side effect of how rmarkdown is working. With bundle it will indeed not work, as with any project folder where you would store Rmd files in subfolders.
However, there is a way to precise this at the doc level. Have you tried setting
output_yaml: "../_output.yaml"
in the header of your posts ? It is not the same but I think it should work as it is a way to pass a specific _output.yaml (or other name) to rmarkdown::render
For supporting the old way you used with Hugo Page bundles, which the blogdown.new_bundle is about, I think it would require some special handling in blogdown. Like an option to set in .Rprofile to indicate where this file would be, or looking for a _output.yaml file in the parent folder if bundles are used but it would then put a rmarkdown logic inside blogdown itself.
Maybe setting this field in the header of all post is easy enough to do ?
I let your try and come back with feedback ! thanks !