I would point out that there was an existing deck present in the same location, and this deck is replacing the old one. The old deck was definitely not up to code since the joist distances were 32 inches, and it had no flashing, and it has structural deficiencies as well (poor design). The current deck has corrected all those deficiencies. Of course I have no expertise, so there could be something out of code that I cannot see.
Would others go to the city at this point and attempt to obtain a permit with the risk of having them find something requiring major additonal work? I am planning to have the 2nd story wall above the deck surfaced with brick, and this time, I definitely make sure that a permit is obtained, so an inspector will be accessing the 2nd story via this new deck (once it is completed) although I guess he would not know that this was newly completed other than by it simply looking new. So an inspector will see the deck. Would such an inspector possibly go out of what they were asked to look at if there are no glaring deficiencies?