How are PDFs made?

No this isn't a question as to how to make a PDF from Indesign. 
The two different export options that exist, Interactive and Print, have different options available.  For example with a Print PDF (not to be confused with printing to a PDF writer) in CS5 you now can't include Interactive elements, you have a choice between Don't Include or Include Appearance.  Dumb IMO.  And with an Interactive PDF you can set the View and Layout defaults.
My question is:  Is there any way to combine the useful bits from both dialogs?  Where does one go to have a look at how Indesign is actually making the PDF?  Or is it completely buried in the program itself?  Is it possible to script?  The only scripts I've seen (admittedly not many) still use Indesigns 'Export Adobe PDF' dialog box.
I tried to see if it would be possible modify the Interactive PDF joboptions file but it doesn't seem to have one, it definitely doesn't give you the option of saving one anyway.  So the  functionality that it offers seems to be unavailable to other ways of exporting.

  In this case it's the mommy Indesign...  So who's the daddy?  Gasp, I'm making b*****d PDFs! 
No, you're simply observing the process of parthenogenesis (if you're of a scientific, aetheistical bent). Or, possibly, you're simply observing the miracle of virgin birth (if not). No PDFs need be insulted by claims of, ah, inadequate parentage, in this situation.

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