"When you have eliminated the impossible, whatever remains, however improbable, must be the truth." -- Sherlock (Arthur Conan Doyle)
Assuming nymag did their research correctly (it seems a pretty simple series of steps), then the most logical conclusion is that someone has a non-public permit. Which points to military or military-adjacent.
However of course clandestine operations are exempted from public permits, which makes this all the more interesting...
The sustained media coverage would help with that.