Unless a PNP issues a nomination under EE stream, or they say they can confirm your non-EE nomination to the EE system, you cannot claim points for PNP (thus say NO on "Do you have PNP" question)
CIC made it clear that more than 1 application of PR under different stream will not affect each other. So I would have no problem having application of PR in EE and PNP at the same time. (Though you will be responsible for fees on both)
Maybe you can write a letter (and provide reference #) about your concurrent PNP application.