Calling Clipboard Markdown to Notes not running

Integration with Notes is pretty limited (on Apple’s end, not ours). Have you seen the Notes integration guide? it would be a good place to understand what can be done to integrate with Notes.

I do not believe Notes has support for creating a note in a specific folder. The Notes app share sheet extension allows you to append to existing notes and create new ones, but not to specify a folder. I believe the same is true for their Shortcuts actions.