I guess I'll have to assume someone sent a threat that maybe included the instructions that a bomb would go off if anyone was allowed to leave the plane. That's the only scenario that makes sense. It's like, "Send 50million crypto coins to this account or else I blow the plane. And if anyone tries to leave, I blow the plane."
However, in every other scenario under the friendly skies, I would say you get all the people off the damn plane FIRST. If it's a ticking time bomb somewhere on board or a passenger with a remote or something volatile in the cargo area, it seems to make sense to get the people out of there.
Imagine being one of the passengers stuck on a plane that has arrived without a problem, then being told by the pilot that there's a maintenance issue (which could obviously be fixed once everyone is off the plane), then being told the pilot lied and it's something else. You assume someone on board is a killer or drug czar. Or that there's a bomb. The last place you want to be is in your seat for three hours, just waiting to see if one of your fellow travelers finally cracks and takes the little kid in row 19 as a hostage. Or the whole plane blows up.
I'm sure this was all done by the book, but it seems to me the book has to be wrong. Since I don't have a background in law enforcement, I might be missing something. I just remember the time I was on the London Underground and saw an unattended bag sitting in the middle of the walkway for several stops, my anxiety skyrocketing until I (a total introvert) started asking every single passenger if the bag was theirs. I was floored by how others didn't seem to think a bag like this was a concern. I was considering picking the luggage up and throwing it (or myself) out the door at the next stop when someone several seats away grabbed it, but that was the most stressful ten minutes of my life because I was sure that bag was going to explode. That's not a feeling I wish on anyone, but many of the passengers in Jacksonville must have felt similarly.
Call me a romantic, but I'd rather see everyone safely off an airplane that might explode even if there's a small chance the perp gets away. It's like a police car chase through a densely-populated part of town: I want the bad guy to get caught, but I don't want others to die just so that can happen.
Anyhow, nothing was found, no one was arrested, and nobody died, so I guess it was "mission accomplished" for federal law enforcement.