That is a very long story with answers that I don't even fully understand yet, but basically the tune has direct control over every single part of the engine, whereas the JB4 only has indirect control over most parts of the engine. For example, APR adjusts the injector duty cycle directly in their tune which allows them to run a much richer AFR and have a higher fueling ceiling in general without maxing out the trims like the JB4 will. Also, APR has directly changed the timing map whereas the JB4 can only indirectly change the timing map by encouraging the ECU to think it's experiencing different conditions than it is. This is only a tiny part of the story.
The biggest advantage of the JB4 is you can adjust things on the fly to suit your car, weather, etc... and can monitor it all quite easily. As you can see in my signature I have both, giving me the best of both worlds. I am not very close to my fueling limit and can run very high boost (at the expense of timing) because of my APR tune, but I have the ability to adjust for my turbo swap and take advantage of e85 because of my JB4.
If you are willing to put a bit of time into tuning with the JB4, and by that I mean a few hours over the course of a week or two, it's really not that hard to work with. The biggest resource we have is George Smooth, who's job at Burger Tuning as far as I can tell is to spend all day every day looking at JB4 logs and telling people what to change to make it better. He's pretty awesome, and basically single handedly is the reason everyone likes the JB4 so much.
