PD4ML can generate TOC and bookmarks (outlines) from H1-H6 structure.

Bookmark structure usually appears in a side frame of Acroread viewer; TOC is inserted as a substitution of tag into the document body.

pd4ml-bookmark-visibility property impacts generation of bookmarks only.

Currently we work on the documentation update, the work is not done yet. But you may take a look to the relevant sections – hopefully it helps:

TOC: http://pd4ml.com/cookbook/pd4ml_table_of_contents.htm
Bookmarks: http://pd4ml.com/cookbook/pdf_bookmarks.htm