No hierarchy structure in PDF output from ditamap

I am trying to publish a ditamap to pdf with FM11. Adobe seems to recommend to save as a FM book with components and then to PDF. Then the hierarchy was lost in the PDF even though it looks very good in the FM book structure.
Almost all topics are rendered as a chapter;
the exception is when the chapter has a href to a dita file;
all sections are rendered as a section no matter where this section belong to and which layer its parent topic is on;
all the topic title use title.0 para tag, and sections use title.1 para tag, so they are all included in the TOC as chapters and sections, no matter which layer they are on in the ditamap;
the numbering of chapter/section are in a mess.
I have looked into the ditafm-output.ini and didn't find useful settings. Any suggestions or clue? or FrameMaker is only not capable for these issues? or can only publish a flat topic PDF?
Thanks!

You might not be accessing the right ditafm-output.ini file. See my answer from Adobe support under:
Publish in Responsive HTML5 - files skipped and 3rd level topics not generated
Hope that helps.
EFR
Cambridge Imaging Systems

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