I doubt just inserting {{delete}} in "the header of" codes shall be helpful...
Maybe I should create its /doc subpage with that?!
Topic on Extension talk:Scribunto/Flow
You're right - leaving the template on the module itself won't add the module page to the relevant category, so doing that won't help. Instead you could put it on the /doc page or the talk page, and explain that it is the module itself that you want deleted. Or you could leave a request on the relevant admin noticeboard. As far as I'm aware, those are the best solutions available at the moment.