It seems you understand the simple chemistry. Do you also understand that the stack test results show that emissions are negligible. Again, that is why they only need a simple air permit which is basically the equivalent of a fan. If there was an issue they would need filters and scrubbers, they don't.
For the last time, JBI will follow the direction given them by the DEC. If you have any problem it seems to be with the DEC, call them. They are okay with the results given them by JBI, hopefully they can ease your mind as well.