As the one who worked on the help files of the two libraries you cited, I can say I don't really know :) haha...

Ok, more seriously, I just did it based on stuff that was out there before. I guess you mentioned the pddp templates? See https://puredata.info/dev/pddp/DraftReferenceDesigns - is that what you are calling outdated? 

Anyway Cyclone 0.2 had this template I'm not sure exactly where it came from, and I just made some variations on it. You can check PD-l2ork's help structure, I guess it came from there... see "all_about_help_patches.pd".

Now, there are some common practices you can get inspired from but no strict rules or golden standard on how to structure your help file... and I'm not really happy with what I have and eventually I could change it a bit...

What I can tell you is that making a good documentation file is hard, takes a lot of time and thought and that it is usually neglected in the Pd world. I cry every time I open a patch with a big mesh of wires all over the place and over messages/objects... sometimes I can't even sleep. Just try to make things clean!!! And document all the messages! Organize it in subpatches if there's too much.

cheers